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HEADER HYDROLASE 22-MAY-23 8JH9
TITLE STRUCTURE-BASED CHARACTERIZATION AND IMPROVEMENT OF AN ENZYMATIC
TITLE 2 ACTIVITY OF ACREMONIUM ALCALOPHILUM FERULOYL ESTERASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: FERULOYL ESTERASE WITH FERULIC ACID;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SODIOMYCES ALCALOPHILUS;
SOURCE 3 ORGANISM_TAXID: 398408;
SOURCE 4 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4922
KEYWDS FERULOYL ESTERASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.PHIENLUPHON,K.KONDO,B.MIKAMI,T.NAGATA,M.KATAHIRA
REVDAT 1 17-APR-24 8JH9 0
JRNL AUTH A.PHIENLUPHON,K.KONDO,B.MIKAMI,K.S.K.TEO,K.SAITO,T.WATANABE,
JRNL AUTH 2 T.NAGATA,M.KATAHIRA
JRNL TITL STRUCTURE-BASED CHARACTERIZATION AND IMPROVEMENT OF AN
JRNL TITL 2 ENZYMATIC ACTIVITY OF ACREMONIUM ALCALOPHILUM FERULOYL
JRNL TITL 3 ESTERASE
JRNL REF ACS SUSTAIN CHEM ENG V. 12 3831 2024
JRNL REFN ESSN 2168-0485
JRNL DOI 10.1021/ACSSUSCHEMENG.3C08222
REMARK 2
REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.20
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) : 2.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.19
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1
REMARK 3 NUMBER OF REFLECTIONS : 16578
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.134
REMARK 3 R VALUE (WORKING SET) : 0.132
REMARK 3 FREE R VALUE : 0.182
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 829
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 41.1900 - 3.6300 0.99 2727 144 0.1147 0.1431
REMARK 3 2 3.6300 - 2.8800 1.00 2671 141 0.1361 0.2091
REMARK 3 3 2.8800 - 2.5200 1.00 2689 141 0.1486 0.1764
REMARK 3 4 2.5200 - 2.2900 1.00 2619 138 0.1414 0.2194
REMARK 3 5 2.2900 - 2.1200 1.00 2649 139 0.1395 0.2251
REMARK 3 6 2.1200 - 2.0000 0.90 2394 126 0.1506 0.1940
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) : 0.170
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.709
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 24.50
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.84
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 : 0.007 2068
REMARK 3 ANGLE : 0.769 2845
REMARK 3 CHIRALITY : 0.057 292
REMARK 3 PLANARITY : 0.006 393
REMARK 3 DIHEDRAL : 14.496 777
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 8JH9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUN-23.
REMARK 100 THE DEPOSITION ID IS D_1300037812.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-FEB-22
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL26B1
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 : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JAN10, 2022
REMARK 200 DATA SCALING SOFTWARE : XDS JAN10, 2022
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16580
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7
REMARK 200 DATA REDUNDANCY : 4.210
REMARK 200 R MERGE (I) : 0.03300
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 30.6300
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12
REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8
REMARK 200 DATA REDUNDANCY IN SHELL : 3.19
REMARK 200 R MERGE FOR SHELL (I) : 0.13300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 10.18
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP 11.7.01
REMARK 200 STARTING MODEL: 8JH8
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 45.56
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2, 0.1 M TRIS-HCL, AND 30%
REMARK 280 (W/V) PEG4,000, PH 8.5, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 293K
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 50.63700
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.28600
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.63700
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.28600
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 APPLY THE FOLLOWING TO CHAINS: A, B
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 MG MG A 302 LIES ON A SPECIAL POSITION.
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 HIS A -5
REMARK 465 HIS A -4
REMARK 465 HIS A -3
REMARK 465 HIS A -2
REMARK 465 HIS A -1
REMARK 465 HIS A 0
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 THR A 205 CA CB OG1 CG2
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 SER A 51 -3.38 75.91
REMARK 500 SER A 51 -2.16 74.62
REMARK 500 SER A 119 -113.00 60.80
REMARK 500 SER A 119 -112.82 60.42
REMARK 500 CYS A 150 96.44 -164.30
REMARK 500
REMARK 500 REMARK: NULL
DBREF 8JH9 A -5 242 PDB 8JH9 8JH9 -5 242
SEQRES 1 A 248 HIS HIS HIS HIS HIS HIS GLN ASN THR ALA GLY CYS GLY
SEQRES 2 A 248 GLN ASN PRO PRO SER SER GLY VAL LYS SER ILE ASN VAL
SEQRES 3 A 248 GLY GLY MET ASN ARG GLU TYR ILE LEU GLN LEU PRO ASN
SEQRES 4 A 248 ASN TYR ASP PRO ASN LYS GLY HIS MET LEU ILE PHE GLY
SEQRES 5 A 248 LEU HIS TRP LEU SER GLY SER MET HIS ASP VAL HIS PRO
SEQRES 6 A 248 ASN TYR TYR GLY LEU ARG GLN LEU ALA GLY ASN ASN ALA
SEQRES 7 A 248 ILE PHE ILE SER PRO ASN GLY ILE ASN ASN GLY TRP ALA
SEQRES 8 A 248 ASN ASP GLY GLY ARG ASP VAL ASN PHE ILE ASP ALA ILE
SEQRES 9 A 248 LEU GLN GLN VAL ARG SER GLN LEU CYS ILE ASN ASP SER
SEQRES 10 A 248 GLN ILE PHE ALA THR GLY PHE SER PHE GLY GLY GLY MET
SEQRES 11 A 248 SER TYR ALA LEU GLY CYS ALA ARG ALA ASN VAL PHE ARG
SEQRES 12 A 248 ALA ILE ALA PRO ILE ALA GLY ALA GLN ILE SER GLY CYS
SEQRES 13 A 248 SER GLY GLY THR SER PRO ILE ALA PHE LEU GLY ILE HIS
SEQRES 14 A 248 GLY THR ASN ASP ASP VAL LEU PRO ILE ALA MET GLY ARG
SEQRES 15 A 248 GLN VAL ARG ASP ARG PHE LEU GLN ASN ASN GLY CYS GLN
SEQRES 16 A 248 PRO LYS ASN ALA PRO GLU PRO GLY TRP GLY GLN GLY PRO
SEQRES 17 A 248 ILE LYS THR GLU TYR SER CYS GLN PRO ASN TYR PRO VAL
SEQRES 18 A 248 THR TRP ILE ALA PHE SER GLY GLY HIS ASP PRO ASN GLN
SEQRES 19 A 248 SER PHE VAL GLY ARG GLU ILE TRP ASP PHE PHE SER GLN
SEQRES 20 A 248 PHE
HET NAG B 1 14
HET NAG B 2 14
HET FER A 301 14
HET MG A 302 1
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETNAM FER 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID
HETNAM MG MAGNESIUM ION
HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA-
HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO-
HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE
HETSYN FER FERULIC ACID
FORMUL 2 NAG 2(C8 H15 N O6)
FORMUL 3 FER C10 H10 O4
FORMUL 4 MG MG 2+
FORMUL 5 HOH *133(H2 O)
HELIX 1 AA1 SER A 53 HIS A 58 1 6
HELIX 2 AA2 ASN A 60 LEU A 64 5 5
HELIX 3 AA3 GLY A 79 GLY A 83 5 5
HELIX 4 AA4 ASN A 86 GLY A 88 5 3
HELIX 5 AA5 GLY A 89 LEU A 106 1 18
HELIX 6 AA6 SER A 119 ARG A 132 1 14
HELIX 7 AA7 PRO A 171 ASN A 186 1 16
HELIX 8 AA8 SER A 229 SER A 240 1 12
SHEET 1 AA1 9 GLY A 14 VAL A 20 0
SHEET 2 AA1 9 MET A 23 GLN A 30 -1 O TYR A 27 N LYS A 16
SHEET 3 AA1 9 ALA A 72 PRO A 77 -1 O PHE A 74 N GLN A 30
SHEET 4 AA1 9 HIS A 41 LEU A 47 1 N MET A 42 O ILE A 73
SHEET 5 AA1 9 ILE A 108 PHE A 118 1 O PHE A 114 N LEU A 43
SHEET 6 AA1 9 ALA A 138 ILE A 142 1 O ILE A 142 N GLY A 117
SHEET 7 AA1 9 ALA A 158 GLY A 164 1 O LEU A 160 N ILE A 139
SHEET 8 AA1 9 VAL A 215 PHE A 220 1 O ILE A 218 N GLY A 161
SHEET 9 AA1 9 ILE A 203 GLU A 206 -1 N THR A 205 O TRP A 217
SSBOND 1 CYS A 6 CYS A 107 1555 1555 2.02
SSBOND 2 CYS A 130 CYS A 150 1555 1555 2.03
SSBOND 3 CYS A 188 CYS A 209 1555 1555 2.01
LINK ND2 ASN A 109 C1 NAG B 1 1555 1555 1.45
LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45
CISPEP 1 HIS A 58 PRO A 59 0 6.09
CRYST1 101.274 38.572 77.878 90.00 125.56 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 0.009874 0.000000 0.007060 0.00000
SCALE2 0.000000 0.025926 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015785 0.00000
TER 1950 PHE A 242
MASTER 244 0 4 8 9 0 0 6 2017 1 49 20
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