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HEADER HYDROLASE 09-SEP-20 7K2Z
TITLE CRYSTAL STRUCTURE OF PISUM SATIVUM KAI2 APO FORM
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PSKAI2B PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PISUM SATIVUM;
SOURCE 3 ORGANISM_TAXID: 3888;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS ENZYME, KARRIKIN, RECEPTOR, A/B HYDROLASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.M.GUERCIO,N.SHABEK
REVDAT 1 16-FEB-22 7K2Z 0
JRNL AUTH A.M.GUERCIO,N.SHABEK
JRNL TITL STRUCTURAL BASIS OF KAI2 DIVERGENCE IN LEGUME
JRNL REF COMMUN BIOL 2022
JRNL REFN ESSN 2399-3642
JRNL DOI 10.1038/S42003-022-03085-6
REMARK 2
REMARK 2 RESOLUTION. 1.61 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.17.1_3660
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 : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.47
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7
REMARK 3 NUMBER OF REFLECTIONS : 34306
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.157
REMARK 3 R VALUE (WORKING SET) : 0.156
REMARK 3 FREE R VALUE : 0.180
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.830
REMARK 3 FREE R VALUE TEST SET COUNT : 2000
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 4.3470 - 3.8700 1.00 2404 149 0.1484 0.1569
REMARK 3 2 3.8700 - 3.0700 1.00 2347 146 0.1431 0.1513
REMARK 3 3 3.0700 - 2.6900 1.00 2342 144 0.1561 0.1926
REMARK 3 4 2.6900 - 2.4400 1.00 2334 145 0.1549 0.1719
REMARK 3 5 2.4400 - 2.2700 1.00 2348 145 0.1520 0.1731
REMARK 3 6 2.2700 - 2.1300 1.00 2324 143 0.1487 0.1803
REMARK 3 7 2.1300 - 2.0300 1.00 2328 145 0.1515 0.1971
REMARK 3 8 2.0300 - 1.9400 1.00 2336 144 0.1579 0.1985
REMARK 3 9 1.9400 - 1.8600 1.00 2339 146 0.1644 0.2076
REMARK 3 10 1.8600 - 1.8000 1.00 2327 144 0.1756 0.2278
REMARK 3 11 1.8000 - 1.7400 1.00 2318 143 0.1743 0.2131
REMARK 3 12 1.7400 - 1.6900 1.00 2329 144 0.1822 0.2166
REMARK 3 13 1.6900 - 1.6500 1.00 2314 144 0.2016 0.2232
REMARK 3 14 1.6500 - 1.6100 0.83 1916 118 0.2366 0.2745
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.540
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.37
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 : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
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 7K2Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-20.
REMARK 100 THE DEPOSITION ID IS D_1000251780.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-OCT-19
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ALS
REMARK 200 BEAMLINE : 8.2.2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34306
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610
REMARK 200 RESOLUTION RANGE LOW (A) : 43.470
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 200 DATA REDUNDANCY : 6.400
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 31.0100
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
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: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHENIX
REMARK 200 STARTING MODEL: 5Z9H
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 45.43
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 2.75% PEG 2000,
REMARK 280 2.75% PEG 3350, 2.75% PEG 4000, 2.75% PEG-ME 5000, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,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 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 43.79750
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.57300
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 43.79750
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.57300
REMARK 290 SMTRY3 4 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 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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 607 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 743 LIES ON A SPECIAL POSITION.
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 THR A 28 -162.67 -124.19
REMARK 500 SER A 95 -124.53 51.99
REMARK 500 ARG A 123 128.85 -171.24
REMARK 500 ASN A 149 89.69 -156.69
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 779 DISTANCE = 7.86 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 400
DBREF 7K2Z A 1 270 PDB 7K2Z 7K2Z 1 270
SEQRES 1 A 270 MET GLY ILE VAL GLU GLU ALA HIS ASN VAL LYS VAL LEU
SEQRES 2 A 270 GLY THR GLY SER ARG PHE ILE VAL LEU ALA HIS GLY PHE
SEQRES 3 A 270 GLY THR ASP GLN SER VAL TRP LYS HIS LEU VAL PRO HIS
SEQRES 4 A 270 LEU LEU GLU GLU PHE ARG VAL ILE LEU TYR ASP ASN MET
SEQRES 5 A 270 GLY ALA GLY THR THR ASN PRO ASP TYR PHE ASP PHE GLU
SEQRES 6 A 270 ARG TYR SER THR LEU GLU GLY TYR ALA TYR ASP LEU LEU
SEQRES 7 A 270 ALA ILE LEU GLN GLU LEU ARG VAL ASP SER CYS ILE PHE
SEQRES 8 A 270 VAL GLY HIS SER VAL SER ALA MET ILE GLY THR VAL ALA
SEQRES 9 A 270 SER ILE SER ARG PRO ASP LEU PHE ALA LYS ILE ILE MET
SEQRES 10 A 270 ILE SER ALA SER PRO ARG TYR LEU ASN ASP SER ASN TYR
SEQRES 11 A 270 PHE GLY GLY PHE GLU GLN GLU ASP LEU ASP GLN LEU PHE
SEQRES 12 A 270 ASN ALA MET ALA SER ASN TYR LYS ALA TRP CYS SER GLY
SEQRES 13 A 270 PHE ALA PRO MET ALA ILE GLY GLY ASP MET GLU SER VAL
SEQRES 14 A 270 ALA VAL GLN GLU PHE SER ARG THR LEU PHE ASN MET ARG
SEQRES 15 A 270 PRO ASP ILE ALA LEU SER VAL LEU GLN THR ILE PHE LYS
SEQRES 16 A 270 SER ASP MET ARG GLN ILE LEU CYS LEU VAL SER VAL PRO
SEQRES 17 A 270 CYS HIS ILE ILE GLN SER MET LYS ASP LEU ALA VAL PRO
SEQRES 18 A 270 VAL VAL VAL ALA GLU TYR LEU HIS GLN HIS VAL GLY THR
SEQRES 19 A 270 GLU SER ILE VAL GLU VAL MET SER THR GLU GLY HIS LEU
SEQRES 20 A 270 PRO GLN LEU SER SER PRO ASP VAL VAL ILE PRO VAL ILE
SEQRES 21 A 270 LEU LYS HIS ILE ARG TYR ASP ILE VAL ALA
HET GOL A 400 6
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 GOL C3 H8 O3
FORMUL 3 HOH *279(H2 O)
HELIX 1 AA1 GLY A 2 HIS A 8 1 7
HELIX 2 AA2 ASP A 29 LYS A 34 5 6
HELIX 3 AA3 LEU A 36 LEU A 40 5 5
HELIX 4 AA4 ASN A 58 PHE A 62 5 5
HELIX 5 AA5 THR A 69 LEU A 84 1 16
HELIX 6 AA6 SER A 95 ARG A 108 1 14
HELIX 7 AA7 GLU A 135 ASN A 149 1 15
HELIX 8 AA8 ASN A 149 GLY A 163 1 15
HELIX 9 AA9 SER A 168 ASN A 180 1 13
HELIX 10 AB1 ARG A 182 LYS A 195 1 14
HELIX 11 AB2 MET A 198 VAL A 205 5 8
HELIX 12 AB3 PRO A 221 VAL A 232 1 12
HELIX 13 AB4 LEU A 247 SER A 252 1 6
HELIX 14 AB5 SER A 252 TYR A 266 1 15
SHEET 1 AA1 7 LYS A 11 LEU A 13 0
SHEET 2 AA1 7 PHE A 44 TYR A 49 -1 O VAL A 46 N LEU A 13
SHEET 3 AA1 7 ARG A 18 ALA A 23 1 N ILE A 20 O ILE A 47
SHEET 4 AA1 7 CYS A 89 HIS A 94 1 O VAL A 92 N VAL A 21
SHEET 5 AA1 7 PHE A 112 ILE A 118 1 O ILE A 116 N PHE A 91
SHEET 6 AA1 7 CYS A 209 LYS A 216 1 O HIS A 210 N MET A 117
SHEET 7 AA1 7 SER A 236 GLU A 244 1 O MET A 241 N GLN A 213
SITE 1 AC1 6 SER A 95 TYR A 124 ILE A 193 HIS A 246
SITE 2 AC1 6 HOH A 529 HOH A 602
CRYST1 87.595 71.146 49.065 90.00 117.62 90.00 C 1 2 1 4
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 0.011416 0.000000 0.005974 0.00000
SCALE2 0.000000 0.014056 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023003 0.00000
TER 2111 ALA A 270
MASTER 251 0 1 14 7 0 2 6 2395 1 6 21
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