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HEADER HYDROLASE 01-NOV-19 6L7N
TITLE CRYSTAL STRUCTURE OF A FUNGAL LIPASES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LIPASE, CLASS 3;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PENICILLIUM ROQUEFORTI FM164;
SOURCE 3 ORGANISM_TAXID: 1365484;
SOURCE 4 STRAIN: FM164;
SOURCE 5 GENE: PROQFM164_S02G000904;
SOURCE 6 EXPRESSION_SYSTEM: PICHIA KUDRIAVZEVII;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4909
KEYWDS LIPASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.H.WANG,H.YUAN,D.M.LAN,X.H.LIU
REVDAT 1 04-NOV-20 6L7N 0
JRNL AUTH Y.H.WANG,H.YUAN,D.M.LAN,X.H.LIU
JRNL TITL CRYSTAL STRUCTURE OF A FUNGAL LIPASES
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.13_2998
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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990
REMARK 3 COMPLETENESS FOR RANGE (%) : 89.6
REMARK 3 NUMBER OF REFLECTIONS : 18008
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.179
REMARK 3 R VALUE (WORKING SET) : 0.176
REMARK 3 FREE R VALUE : 0.228
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190
REMARK 3 FREE R VALUE TEST SET COUNT : 934
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 10.0000 - 3.4400 0.92 2509 132 0.1645 0.1966
REMARK 3 2 3.4400 - 2.7300 0.97 2661 139 0.1694 0.2130
REMARK 3 3 2.7300 - 2.3900 0.97 2653 116 0.1796 0.2151
REMARK 3 4 2.3900 - 2.1700 0.82 2252 122 0.1812 0.2412
REMARK 3 5 2.1700 - 2.0100 0.94 2540 162 0.1749 0.2321
REMARK 3 6 2.0100 - 1.8900 0.75 2065 113 0.2041 0.3096
REMARK 3 7 1.8900 - 1.8000 0.89 2394 150 0.1998 0.2925
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
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) : 0.224
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.376
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 12.31
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.58
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 : 0.008 2132
REMARK 3 ANGLE : 0.888 2918
REMARK 3 CHIRALITY : 0.055 322
REMARK 3 PLANARITY : 0.006 378
REMARK 3 DIHEDRAL : 8.171 1658
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 6L7N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-NOV-19.
REMARK 100 THE DEPOSITION ID IS D_1300014344.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-MAY-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 : SSRF
REMARK 200 BEAMLINE : BL18U1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000
REMARK 200 DATA SCALING SOFTWARE : HKL-3000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19035
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
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 (%) : 94.3
REMARK 200 DATA REDUNDANCY : 3.400
REMARK 200 R MERGE (I) : 0.03900
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 23.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.10000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 12.26
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 1DT3
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 32.27
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG 1500, 0.1 M SODIUM ACETATE PH
REMARK 280 4.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,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
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
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 GLU A -1
REMARK 465 PHE A 0
REMARK 465 ASN A 271
REMARK 465 ASP A 272
REMARK 465 GLY A 273
REMARK 465 ARG A 274
REMARK 465 PRO A 275
REMARK 465 PHE A 276
REMARK 465 LYS A 277
REMARK 465 ARG A 278
REMARK 465 VAL A 279
REMARK 465 VAL A 280
REMARK 465 ASP A 281
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 566 O HOH A 588 1.82
REMARK 500 O HOH A 454 O HOH A 464 1.87
REMARK 500 O HOH A 309 O HOH A 436 1.89
REMARK 500 O HOH A 344 O HOH A 480 2.03
REMARK 500 O HOH A 366 O HOH A 512 2.05
REMARK 500 O HOH A 492 O HOH A 550 2.08
REMARK 500 O HOH A 329 O HOH A 507 2.09
REMARK 500 O HOH A 471 O HOH A 585 2.10
REMARK 500 NE2 HIS A 184 O HOH A 301 2.11
REMARK 500 OD2 ASP A 109 O HOH A 302 2.13
REMARK 500 NE2 GLN A 9 O HOH A 303 2.16
REMARK 500 O HOH A 425 O HOH A 582 2.17
REMARK 500 O HOH A 338 O HOH A 376 2.17
REMARK 500 OH TYR A 97 O MET A 209 2.17
REMARK 500 O PHE A 95 O HOH A 304 2.18
REMARK 500 O THR A 227 O HOH A 305 2.18
REMARK 500 OE1 GLU A 74 O HOH A 306 2.19
REMARK 500 O HOH A 325 O HOH A 544 2.19
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 ALA A 58 -159.95 -167.98
REMARK 500 ASP A 92 -2.30 -144.33
REMARK 500 SER A 145 -142.95 62.69
REMARK 500 ALA A 177 -173.46 -170.03
REMARK 500 THR A 197 -113.83 33.82
REMARK 500 ASP A 199 123.26 -39.02
REMARK 500 PHE A 263 -53.50 71.24
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 592 DISTANCE = 6.03 ANGSTROMS
REMARK 525 HOH A 593 DISTANCE = 6.49 ANGSTROMS
REMARK 525 HOH A 594 DISTANCE = 7.12 ANGSTROMS
DBREF 6L7N A 1 279 UNP W6Q990 W6Q990_PENRF 27 305
SEQADV 6L7N GLU A -1 UNP W6Q990 EXPRESSION TAG
SEQADV 6L7N PHE A 0 UNP W6Q990 EXPRESSION TAG
SEQADV 6L7N VAL A 280 UNP W6Q990 EXPRESSION TAG
SEQADV 6L7N ASP A 281 UNP W6Q990 EXPRESSION TAG
SEQRES 1 A 283 GLU PHE ASP VAL SER THR SER GLU LEU ASN GLN PHE ASP
SEQRES 2 A 283 PHE TRP VAL GLN TYR ALA ALA ALA ALA TYR TYR ALA ASP
SEQRES 3 A 283 ASP TYR THR ALA GLN VAL GLY ALA LYS ILE SER CYS SER
SEQRES 4 A 283 LYS GLY ASN CYS PRO GLN VAL GLU GLU ALA GLY ALA THR
SEQRES 5 A 283 VAL PHE TYR ASP PHE SER ASN ALA THR ILE THR ASP THR
SEQRES 6 A 283 SER GLY PHE ILE ALA VAL ASP HIS ALA ASN GLU ALA VAL
SEQRES 7 A 283 VAL LEU SER PHE ARG GLY SER TYR SER VAL ARG ASN TRP
SEQRES 8 A 283 VAL SER ASP ALA ILE PHE VAL TYR THR ASN PRO ASP LEU
SEQRES 9 A 283 CYS ASP GLY CYS LEU ALA ASP LEU GLY PHE TRP GLY SER
SEQRES 10 A 283 TRP VAL LEU VAL ARG ASP ASP ILE ILE LYS GLU LEU LYS
SEQRES 11 A 283 GLU ALA VAL SER GLN ASN PRO GLY TYR GLU LEU ALA VAL
SEQRES 12 A 283 VAL GLY HIS SER LEU GLY ALA ALA VAL ALA THR LEU ALA
SEQRES 13 A 283 VAL ALA ASP LEU ARG GLY LYS GLY TYR PRO SER ALA LYS
SEQRES 14 A 283 LEU TYR ALA TYR ALA SER PRO ARG VAL ALA ASN VAL PRO
SEQRES 15 A 283 LEU ALA LYS HIS ILE THR ALA GLN GLY ASN ASN TYR ARG
SEQRES 16 A 283 PHE THR HIS THR ASP ASP PRO VAL PRO LYS LEU PRO LEU
SEQRES 17 A 283 LEU ALA MET GLY TYR VAL HIS ILE SER PRO GLU TYR TRP
SEQRES 18 A 283 ILE THR SER PRO ASN ASN VAL THR VAL GLY ALA SER ASP
SEQRES 19 A 283 ILE LYS VAL ILE ASP GLY ASP ILE SER PHE ALA GLY ASN
SEQRES 20 A 283 THR GLY THR GLY LEU PRO SER LEU GLU ASP PHE GLU ALA
SEQRES 21 A 283 HIS LYS TRP TYR PHE MET LYS THR ASP ALA GLY LYS ASN
SEQRES 22 A 283 ASP GLY ARG PRO PHE LYS ARG VAL VAL ASP
FORMUL 2 HOH *294(H2 O)
HELIX 1 AA1 SER A 3 TYR A 21 1 19
HELIX 2 AA2 TYR A 22 THR A 27 1 6
HELIX 3 AA3 CYS A 41 ALA A 47 1 7
HELIX 4 AA4 SER A 85 ALA A 93 1 9
HELIX 5 AA5 LEU A 110 ASN A 134 1 25
HELIX 6 AA6 SER A 145 GLY A 160 1 16
HELIX 7 AA7 VAL A 179 GLY A 189 1 11
HELIX 8 AA8 PRO A 200 LEU A 204 5 5
HELIX 9 AA9 LEU A 206 MET A 209 5 4
HELIX 10 AB1 GLY A 229 SER A 231 5 3
HELIX 11 AB2 ALA A 243 THR A 248 1 6
HELIX 12 AB3 SER A 252 LYS A 260 5 9
SHEET 1 AA1 8 THR A 50 PHE A 55 0
SHEET 2 AA1 8 SER A 64 ASP A 70 -1 O ILE A 67 N PHE A 52
SHEET 3 AA1 8 ALA A 75 ARG A 81 -1 O ALA A 75 N ASP A 70
SHEET 4 AA1 8 GLU A 138 HIS A 144 1 O GLU A 138 N VAL A 76
SHEET 5 AA1 8 LYS A 167 TYR A 171 1 O LYS A 167 N LEU A 139
SHEET 6 AA1 8 ASN A 191 HIS A 196 1 O TYR A 192 N LEU A 168
SHEET 7 AA1 8 GLU A 217 ILE A 220 1 O ILE A 220 N THR A 195
SHEET 8 AA1 8 ILE A 233 ILE A 236 -1 O LYS A 234 N TRP A 219
SHEET 1 AA2 2 TYR A 97 THR A 98 0
SHEET 2 AA2 2 ALA A 108 ASP A 109 -1 O ALA A 108 N THR A 98
SHEET 1 AA3 2 ALA A 177 ASN A 178 0
SHEET 2 AA3 2 TYR A 211 VAL A 212 -1 O VAL A 212 N ALA A 177
SSBOND 1 CYS A 36 CYS A 41 1555 1555 2.04
SSBOND 2 CYS A 103 CYS A 106 1555 1555 2.02
CISPEP 1 LEU A 204 PRO A 205 0 -11.57
CISPEP 2 SER A 215 PRO A 216 0 -1.83
CRYST1 33.247 44.928 46.025 109.22 101.36 112.10 P 1 1
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 0.030078 0.012213 0.012796 0.00000
SCALE2 0.000000 0.024023 0.011903 0.00000
SCALE3 0.000000 0.000000 0.024733 0.00000
TER 2067 LYS A 270
MASTER 267 0 0 12 12 0 0 6 2360 1 4 22
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