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HEADER HYDROLASE 09-FEB-21 7E3Z
TITLE NON-RIBOSOMAL PEPTIDE SYNTHETASES, THIOESTERASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: THIOESTERASE;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES SP. SNM55;
SOURCE 3 ORGANISM_TAXID: 1571707;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS NON-RIBOSOMAL PEPTIDE SYNTHETASES, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.E.JUNG,S.S.CHA
REVDAT 1 22-DEC-21 7E3Z 0
JRNL AUTH M.S.KIM,M.BAE,Y.E.JUNG,J.M.KIM,S.HWANG,M.C.SONG,Y.H.BAN,
JRNL AUTH 2 E.S.BAE,S.HONG,S.K.LEE,S.S.CHA,D.C.OH,Y.J.YOON
JRNL TITL UNPRECEDENTED NONCANONICAL FEATURES OF THE NONLINEAR
JRNL TITL 2 NONRIBOSOMAL PEPTIDE SYNTHETASE ASSEMBLY LINE FOR WS9326A
JRNL TITL 3 BIOSYNTHESIS.
JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 60 19766 2021
JRNL REFN ESSN 1521-3773
JRNL PMID 33963654
JRNL DOI 10.1002/ANIE.202103872
REMARK 2
REMARK 2 RESOLUTION. 1.45 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.10.1
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.07
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7
REMARK 3 NUMBER OF REFLECTIONS : 41783
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.181
REMARK 3 R VALUE (WORKING SET) : 0.180
REMARK 3 FREE R VALUE : 0.203
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2090
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 1.4837 - 1.4500 0.96 0 0 0.2292 0.2671
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : NULL
REMARK 3 SHRINKAGE RADIUS : NULL
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.42
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.013 1928
REMARK 3 ANGLE : 1.396 2640
REMARK 3 CHIRALITY : 0.106 289
REMARK 3 PLANARITY : 0.009 349
REMARK 3 DIHEDRAL : 17.144 689
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 7E3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-FEB-21.
REMARK 100 THE DEPOSITION ID IS D_1300020719.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-NOV-20
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PAL/PLS
REMARK 200 BEAMLINE : 5C (4A)
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.98
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42069
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450
REMARK 200 RESOLUTION RANGE LOW (A) : 29.070
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7
REMARK 200 DATA REDUNDANCY : 7.000
REMARK 200 R MERGE (I) : 0.06800
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 15.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 43.13
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, 0.05M CALCL2, 30% PEG
REMARK 280 M550, PH 6.5, MICROBATCH, TEMPERATURE 289K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 33.22500
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 150 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11110 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 1
REMARK 465 ALA A 2
REMARK 465 THR A 3
REMARK 465 ILE A 4
REMARK 465 VAL A 5
REMARK 465 ASN A 6
REMARK 465 THR A 7
REMARK 465 ALA A 8
REMARK 465 ALA A 9
REMARK 465 ARG A 133
REMARK 465 GLU A 134
REMARK 465 GLY A 259
REMARK 465 THR A 260
REMARK 465 ARG A 261
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLU A 23 CG CD OE1 OE2
REMARK 470 ARG A 132 CG CD NE CZ NH1 NH2
REMARK 470 MET A 135 CG SD CE
REMARK 470 ARG A 137 CG CD NE CZ NH1 NH2
REMARK 470 GLU A 138 CG CD OE1 OE2
REMARK 470 GLU A 167 CG CD OE1 OE2
REMARK 470 GLU A 169 CG CD OE1 OE2
REMARK 470 LYS A 172 CG CD CE NZ
REMARK 470 GLU A 241 CG CD OE1 OE2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O HOH A 597 O HOH A 602 2.03
REMARK 500 NH1 ARG A 15 O HOH A 401 2.08
REMARK 500 OE1 GLN A 14 NH2 ARG A 40 2.09
REMARK 500 O HOH A 530 O HOH A 585 2.12
REMARK 500 O HOH A 517 O HOH A 545 2.16
REMARK 500 O HOH A 433 O HOH A 574 2.18
REMARK 500 O GLY A 205 O HOH A 402 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 MET A 98 CG - SD - CE ANGL. DEV. = -21.5 DEGREES
REMARK 500 ARG A 201 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 GLU A 61 -133.80 54.80
REMARK 500 SER A 97 -120.29 61.59
REMARK 500 TYR A 238 -134.43 58.62
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 301
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE SEQUENCE HAS BEEN DEPOSITED TO GENBAND WITH ACCESSION NUMBER
REMARK 999 QBA57731.1.
DBREF 7E3Z A 1 261 PDB 7E3Z 7E3Z 1 261
SEQRES 1 A 261 MET ALA THR ILE VAL ASN THR ALA ALA GLY ALA ALA VAL
SEQRES 2 A 261 GLN ARG PRO ARG PRO ARG PRO GLY ALA GLU ARG VAL LEU
SEQRES 3 A 261 VAL CYS LEU SER TYR CYS GLY GLY GLY THR ALA PRO PHE
SEQRES 4 A 261 ARG GLN TRP ALA GLU ASP LEU PRO GLU ASP VAL GLU LEU
SEQRES 5 A 261 ALA LEU ILE CYS TYR PRO GLY ARG GLU ALA ARG PHE GLY
SEQRES 6 A 261 ALA PRO PHE ALA ARG VAL TRP THR GLU LEU ARG ASP ASP
SEQRES 7 A 261 VAL VAL ARG SER VAL ARG GLY LEU THR GLY ARG PRO TYR
SEQRES 8 A 261 ILE LEU PHE GLY HIS SER MET GLY SER TRP MET ALA PHE
SEQRES 9 A 261 GLU THR ALA ALA GLU LEU GLU ARG ILE GLY ALA ALA PRO
SEQRES 10 A 261 PRO GLU ALA LEU VAL VAL SER GLY GLY VAL ALA PRO HIS
SEQRES 11 A 261 LYS ARG ARG GLU MET PRO ARG GLU ASP THR PRO ARG SER
SEQRES 12 A 261 ASP ALA ASP MET ASP ALA LEU VAL ARG TRP MET ARG ASP
SEQRES 13 A 261 LEU GLY GLN VAL SER PRO ALA ILE ALA ALA GLU PRO GLU
SEQRES 14 A 261 LEU LEU LYS ILE ALA VAL ASP LEU LEU ARG ALA ASP LEU
SEQRES 15 A 261 ALA VAL THR GLU SER TYR ARG PHE VAL ASP GLY THR ARG
SEQRES 16 A 261 VAL SER VAL PRO LEU ARG VAL LEU TYR GLY THR GLU ASP
SEQRES 17 A 261 ALA ALA PRO PHE ALA ASP VAL GLU ARG HIS TRP ARG PRO
SEQRES 18 A 261 LEU THR ALA GLY PRO PHE GLN ALA VAL GLU LEU PRO GLY
SEQRES 19 A 261 GLY HIS PHE TYR THR PRO GLU VAL TRP ALA ARG LEU THR
SEQRES 20 A 261 GLU TRP CYS THR LEU PRO VAL PRO GLY ALA ALA GLY THR
SEQRES 21 A 261 ARG
HET CL A 301 1
HETNAM CL CHLORIDE ION
FORMUL 2 CL CL 1-
FORMUL 3 HOH *214(H2 O)
HELIX 1 AA1 THR A 36 ASP A 45 5 10
HELIX 2 AA2 ARG A 60 PHE A 64 5 5
HELIX 3 AA3 VAL A 71 GLY A 85 1 15
HELIX 4 AA4 SER A 97 GLY A 114 1 18
HELIX 5 AA5 ALA A 128 ARG A 132 5 5
HELIX 6 AA6 PRO A 136 THR A 140 5 5
HELIX 7 AA7 ASP A 146 GLY A 158 1 13
HELIX 8 AA8 SER A 161 ALA A 166 1 6
HELIX 9 AA9 GLU A 167 SER A 187 1 21
HELIX 10 AB1 PRO A 211 ARG A 220 1 10
HELIX 11 AB2 PRO A 221 THR A 223 5 3
HELIX 12 AB3 THR A 239 ARG A 245 1 7
HELIX 13 AB4 THR A 247 LEU A 252 1 6
SHEET 1 AA1 6 VAL A 50 LEU A 54 0
SHEET 2 AA1 6 ARG A 24 LEU A 29 1 N LEU A 26 O ALA A 53
SHEET 3 AA1 6 TYR A 91 HIS A 96 1 O ILE A 92 N VAL A 27
SHEET 4 AA1 6 ALA A 120 SER A 124 1 O VAL A 122 N LEU A 93
SHEET 5 AA1 6 LEU A 200 GLY A 205 1 O LEU A 203 N VAL A 123
SHEET 6 AA1 6 PHE A 227 LEU A 232 1 O VAL A 230 N VAL A 202
SITE 1 AC1 3 CYS A 32 SER A 97 MET A 98
CRYST1 40.730 66.450 45.290 90.00 98.06 90.00 P 1 21 1 2
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.024552 0.000000 0.003477 0.00000
SCALE2 0.000000 0.015049 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022300 0.00000
TER 1875 ALA A 258
MASTER 285 0 1 13 6 0 1 6 2089 1 0 21
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