HEADER OXIDOREDUCTASE 14-OCT-07 2VDZ OBSLTE 12-OCT-11 2VDZ 4A2E TITLE CRYSTAL STRUCTURE OF A CORIOLOPSIS GALLICA LACCASE AT 1.7 A TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACCASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.10.3.2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORIOLOPSIS GALLICA; SOURCE 3 ORGANISM_TAXID: 76126 KEYWDS OXIDOREDUCTASE, BLUE MULTICCOPER OXIDASE, CATALYTICAL KEYWDS 2 INTERMEDIARY, COPPER, METAL-BINDING, PHENOL OXIDASE EXPDTA X-RAY DIFFRACTION AUTHOR E.DE LA MORA,B.VALDERRAMA,E.HORJALES,E.RUDINO-PINERA REVDAT 3 12-OCT-11 2VDZ 1 OBSLTE REVDAT 2 24-FEB-09 2VDZ 1 VERSN REVDAT 1 04-NOV-08 2VDZ 0 JRNL AUTH E.DE LA MORA,B.VALDERRAMA,E.HORJALES, JRNL AUTH 2 E.RUDINO-PINERA JRNL TITL CRYSTAL STRUCTURE OF CORIOLOPSIS GALLICA LACCASE JRNL TITL 2 AT 1.7 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.200 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 73206 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3877 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4399 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 242 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3800 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.96000 REMARK 3 B22 (A**2) : 0.83000 REMARK 3 B33 (A**2) : 0.13000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.098 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.074 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.863 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3984 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5502 ; 1.494 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 515 ;17.198 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 174 ;35.308 ;24.540 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 515 ;11.784 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;19.842 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 629 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3153 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1895 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2682 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 516 ; 0.112 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 48 ; 0.194 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.113 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2583 ; 0.811 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4108 ; 1.252 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1580 ; 2.059 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1390 ; 2.854 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2VDZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-OCT-07. REMARK 100 THE PDBE ID CODE IS EBI-34144. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : YALE REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU-MSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80314 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.70 REMARK 200 RESOLUTION RANGE LOW (A) : 26.45 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.2 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 3.2 REMARK 200 R MERGE (I) : 0.05 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.50 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.4 REMARK 200 R MERGE FOR SHELL (I) : 0.30 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.20 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: PDB ENTRY 1V10 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.4 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1000, PEG8000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 28.19100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.32250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.06400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.32250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.19100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.06400 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 GENERATING THE BIOMOLECULE 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: PQS 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 REMARK 500 O HOH A 2597 O HOH A 2694 4545 2.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLN A 496 C GLN A 496 OXT 0.222 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 ALA A 160 N - CA - C ANGL. DEV. = -25.4 DEGREES REMARK 500 LEU A 325 N - CA - C ANGL. DEV. = 18.8 DEGREES REMARK 500 LEU A 365 N - CA - C ANGL. DEV. = -18.9 DEGREES REMARK 500 ASP A 494 N - CA - C ANGL. DEV. = -16.5 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 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 LEU A 58 120.47 77.60 REMARK 500 SER A 113 -136.81 49.64 REMARK 500 ASP A 141 -165.56 -160.33 REMARK 500 ASP A 205 -73.46 -156.38 REMARK 500 ALA A 240 -9.59 83.10 REMARK 500 GLN A 267 53.79 -111.85 REMARK 500 LEU A 365 115.79 -163.48 REMARK 500 PHE A 392 130.00 -2.08 REMARK 500 ASN A 418 50.04 -154.13 REMARK 500 ARG A 422 -168.44 -161.28 REMARK 500 ASN A 442 81.81 -152.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 159 ALA A 160 -111.83 REMARK 500 ALA A 312 PRO A 313 136.27 REMARK 500 ALA A 324 LEU A 325 135.76 REMARK 500 LEU A 364 LEU A 365 -115.91 REMARK 500 ALA A 389 PRO A 390 -136.22 REMARK 500 GLY A 391 PHE A 392 100.31 REMARK 500 VAL A 477 PRO A 478 146.66 REMARK 500 PRO A 493 ASP A 494 -136.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ALA A 160 46.4 L L OUTSIDE RANGE REMARK 500 LEU A 325 23.8 L L OUTSIDE RANGE REMARK 500 PHE A 392 17.3 L L OUTSIDE RANGE 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 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A1497 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 66 ND1 REMARK 620 2 HIS A 451 NE2 112.5 REMARK 620 3 HIS A 109 NE2 142.3 102.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A1498 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 111 NE2 REMARK 620 2 HIS A 449 NE2 115.3 REMARK 620 3 HOH A2612 O 89.3 114.4 REMARK 620 4 HIS A 399 NE2 112.1 120.7 99.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A1500 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 455 ND1 REMARK 620 2 HIS A 394 ND1 101.1 REMARK 620 3 CYS A 450 SG 132.9 125.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A1497 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A1498 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A1499 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A1500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A1504 REMARK 999 REMARK 999 SEQUENCE REMARK 999 SOME RESIDUES ARE DIFFERENT FROM SEQUENCE. HOWEVER, THE REMARK 999 IDENTITY IS 96 PER CENT TO SEQUENCE ABD93941 (UNIPROT) DBREF 2VDZ A 1 496 PDB 2VDZ 2VDZ 1 496 SEQRES 1 A 496 ALA ILE GLY PRO VAL ALA ASP LEU THR ILE SER ASN GLY SEQRES 2 A 496 ALA VAL SER PRO ASP GLY PHE SER ARG GLN ALA ILE LEU SEQRES 3 A 496 VAL ASN ASP VAL PHE PRO SER PRO LEU ILE THR GLY ASN SEQRES 4 A 496 LYS GLY ASP ARG PHE GLN LEU ASN VAL ILE ASP ASN MET SEQRES 5 A 496 THR ASN HIS THR MET LEU LYS SER THR SER ILE HIS TRP SEQRES 6 A 496 HIS GLY PHE PHE GLN HIS GLY THR ASN TRP ALA ASP GLY SEQRES 7 A 496 PRO ALA PHE VAL ASN GLN CYS PRO ILE SER THR GLY HIS SEQRES 8 A 496 ALA PHE LEU TYR ASP PHE GLN VAL PRO ASP GLN ALA GLY SEQRES 9 A 496 THR PHE TRP TYR HIS SER HIS LEU SER THR GLN TYR CYS SEQRES 10 A 496 ASP GLY LEU ARG GLY PRO ILE VAL VAL TYR ASP PRO ASN SEQRES 11 A 496 ASP PRO HIS ALA SER LEU TYR ASP VAL ASP ASP ASP SER SEQRES 12 A 496 THR VAL ILE THR LEU ALA ASP TRP TYR HIS LEU ALA ALA SEQRES 13 A 496 LYS VAL GLY ALA PRO VAL PRO THR ALA ASP ALA THR LEU SEQRES 14 A 496 ILE ASN GLY LEU GLY ARG SER ALA ALA THR LEU ALA ALA SEQRES 15 A 496 ASP LEU ALA VAL ILE THR VAL THR LYS GLY LYS ARG TYR SEQRES 16 A 496 ARG PHE ARG LEU VAL SER LEU SER CYS ASP PRO ASN TYR SEQRES 17 A 496 THR PHE SER ILE ASP GLY HIS SER LEU THR VAL ILE GLU SEQRES 18 A 496 ALA ASP SER VAL ASN LEU LYS PRO HIS THR VAL ASP SER SEQRES 19 A 496 LEU GLN ILE PHE ALA ALA GLN ARG TYR SER PHE VAL LEU SEQRES 20 A 496 ASN ALA ASP GLN ASP VAL ASP ASN TYR TRP ILE ARG ALA SEQRES 21 A 496 LEU PRO ASN SER GLY THR GLN ASN PHE ALA GLY GLY THR SEQRES 22 A 496 ASN SER ALA ILE LEU ARG TYR ASP GLY ALA ALA PRO VAL SEQRES 23 A 496 GLU PRO THR THR SER GLN THR PRO SER THR ASN PRO LEU SEQRES 24 A 496 VAL GLU SER ALA LEU THR THR LEU LYS GLY THR ALA ALA SEQRES 25 A 496 PRO GLY SER PRO THR PRO GLY GLY VAL ASP LEU ALA LEU SEQRES 26 A 496 ASN MET ALA PHE GLY PHE ALA GLY GLY ASN PHE THR ILE SEQRES 27 A 496 ASN GLY ALA SER PHE THR PRO PRO THR VAL PRO VAL LEU SEQRES 28 A 496 LEU GLN ILE LEU SER GLY ALA GLN SER ALA ALA ASP LEU SEQRES 29 A 496 LEU PRO ALA GLY SER VAL TYR SER LEU PRO ALA ASN ALA SEQRES 30 A 496 ASP ILE GLU ILE SER LEU PRO ALA THR ALA ALA ALA PRO SEQRES 31 A 496 GLY PHE PRO HIS PRO PHE HIS LEU HIS GLY HIS VAL PHE SEQRES 32 A 496 ALA VAL VAL ARG SER ALA GLY SER SER THR TYR ASN TYR SEQRES 33 A 496 ALA ASN PRO VAL TYR ARG ASP VAL VAL SER THR GLY ALA SEQRES 34 A 496 PRO GLY ASP ASN VAL THR ILE ARG PHE ARG THR ASP ASN SEQRES 35 A 496 PRO GLY PRO TRP PHE LEU HIS CYS HIS ILE ASP PHE HIS SEQRES 36 A 496 LEU GLU ALA GLY PHE ALA VAL VAL MET ALA GLU ASP ILE SEQRES 37 A 496 PRO ASP VAL ALA ALA THR ASN PRO VAL PRO GLN ALA TRP SEQRES 38 A 496 SER ASP LEU CYS PRO THR TYR ASP ALA LEU SER PRO ASP SEQRES 39 A 496 ASP GLN HET CU A1497 1 HET CU A1498 1 HET CU A1499 1 HET CU A1500 1 HET NAG A1501 14 HET NAG A1502 14 HET NAG A1503 14 HET NAG A1504 14 HETNAM CU COPPER (II) ION HETNAM NAG N-ACETYL-D-GLUCOSAMINE FORMUL 2 CU 4(CU 2+) FORMUL 3 NAG 4(C8 H15 N O6) FORMUL 4 HOH *740(H2 O1) HELIX 1 1 ASN A 54 LEU A 58 5 5 HELIX 2 2 THR A 73 ASP A 77 5 5 HELIX 3 3 THR A 114 GLY A 119 5 6 HELIX 4 4 HIS A 133 TYR A 137 5 5 HELIX 5 5 ASP A 141 SER A 143 5 3 HELIX 6 6 PHE A 269 THR A 273 5 5 HELIX 7 7 VAL A 300 LEU A 304 5 5 HELIX 8 8 PRO A 349 SER A 356 1 8 HELIX 9 9 ILE A 452 ALA A 458 1 7 HELIX 10 10 ASP A 470 ASN A 475 1 6 HELIX 11 11 PRO A 478 ASP A 483 1 6 HELIX 12 12 ASP A 483 ALA A 490 1 8 HELIX 13 13 SER A 492 GLN A 496 5 5 SHEET 1 AA 4 ARG A 22 VAL A 27 0 SHEET 2 AA 4 VAL A 5 VAL A 15 -1 O SER A 11 N LEU A 26 SHEET 3 AA 4 ARG A 43 ASP A 50 1 O GLN A 45 N ALA A 6 SHEET 4 AA 4 HIS A 91 GLN A 98 -1 O HIS A 91 N ASP A 50 SHEET 1 AB 4 ILE A 36 ASN A 39 0 SHEET 2 AB 4 ARG A 121 TYR A 127 1 O PRO A 123 N ILE A 36 SHEET 3 AB 4 GLY A 104 SER A 110 -1 O GLY A 104 N VAL A 126 SHEET 4 AB 4 ILE A 63 HIS A 66 -1 O HIS A 64 N HIS A 109 SHEET 1 AC 6 ALA A 167 ILE A 170 0 SHEET 2 AC 6 VAL A 145 TRP A 151 -1 O ALA A 149 N LEU A 169 SHEET 3 AC 6 ARG A 194 SER A 201 1 O ARG A 198 N ILE A 146 SHEET 4 AC 6 ARG A 242 ASN A 248 -1 O TYR A 243 N LEU A 199 SHEET 5 AC 6 LEU A 217 ALA A 222 -1 O THR A 218 N VAL A 246 SHEET 6 AC 6 VAL A 225 VAL A 232 -1 O VAL A 225 N ALA A 222 SHEET 1 AD 5 VAL A 186 VAL A 189 0 SHEET 2 AD 5 SER A 275 TYR A 280 1 O ILE A 277 N ILE A 187 SHEET 3 AD 5 ASN A 255 PRO A 262 -1 O TYR A 256 N LEU A 278 SHEET 4 AD 5 TYR A 208 ILE A 212 -1 O THR A 209 N LEU A 261 SHEET 5 AD 5 LEU A 235 ILE A 237 -1 O LEU A 235 N PHE A 210 SHEET 1 AE 5 LEU A 323 ASN A 326 0 SHEET 2 AE 5 ASP A 378 PRO A 384 1 O ASP A 378 N LEU A 323 SHEET 3 AE 5 ASN A 433 ARG A 439 -1 O VAL A 434 N LEU A 383 SHEET 4 AE 5 PHE A 403 ARG A 407 -1 O ALA A 404 N ARG A 437 SHEET 5 AE 5 TYR A 421 ARG A 422 -1 O ARG A 422 N PHE A 403 SHEET 1 AF 2 PHE A 329 ALA A 332 0 SHEET 2 AF 2 ASN A 335 ILE A 338 -1 O ASN A 335 N ALA A 332 SHEET 1 AG 5 VAL A 370 LEU A 373 0 SHEET 2 AG 5 ALA A 461 GLU A 466 1 O VAL A 463 N TYR A 371 SHEET 3 AG 5 GLY A 444 CYS A 450 -1 O GLY A 444 N GLU A 466 SHEET 4 AG 5 PRO A 395 LEU A 398 -1 O HIS A 397 N HIS A 449 SHEET 5 AG 5 VAL A 424 SER A 426 -1 O VAL A 425 N PHE A 396 SSBOND 1 CYS A 85 CYS A 485 1555 1555 2.09 SSBOND 2 CYS A 117 CYS A 204 1555 1555 2.04 LINK ND2 ASN A 54 C1 NAG A1501 1555 1555 1.44 LINK ND2 ASN A 433 C1 NAG A1503 1555 1555 1.45 LINK CU CU A1497 NE2 HIS A 109 1555 1555 2.22 LINK CU CU A1497 ND1 HIS A 66 1555 1555 2.03 LINK CU CU A1497 NE2 HIS A 451 1555 1555 2.20 LINK CU CU A1498 O HOH A2612 1555 1555 2.28 LINK CU CU A1498 NE2 HIS A 399 1555 1555 2.07 LINK CU CU A1498 NE2 HIS A 449 1555 1555 2.04 LINK CU CU A1498 NE2 HIS A 111 1555 1555 2.06 LINK CU CU A1499 NE2 HIS A 64 1555 1555 1.78 LINK CU CU A1500 SG CYS A 450 1555 1555 2.22 LINK CU CU A1500 ND1 HIS A 394 1555 1555 2.10 LINK CU CU A1500 ND1 HIS A 455 1555 1555 2.11 LINK O4 NAG A1501 C1 NAG A1502 1555 1555 1.44 LINK O4 NAG A1503 C1 NAG A1504 1555 1555 1.44 CISPEP 1 GLY A 3 PRO A 4 0 6.86 CISPEP 2 PHE A 31 PRO A 32 0 -2.11 CISPEP 3 LEU A 365 PRO A 366 0 9.67 CISPEP 4 PHE A 392 PRO A 393 0 -0.21 SITE 1 AC1 6 HIS A 64 HIS A 66 TRP A 107 HIS A 109 SITE 2 AC1 6 HIS A 451 HOH A2612 SITE 1 AC2 5 HIS A 111 HIS A 397 HIS A 399 HIS A 449 SITE 2 AC2 5 HOH A2612 SITE 1 AC3 5 HIS A 64 HIS A 66 HIS A 397 HIS A 399 SITE 2 AC3 5 HOH A2149 SITE 1 AC4 4 HIS A 394 CYS A 450 ILE A 452 HIS A 455 SITE 1 AC5 8 GLN A 23 ASN A 54 MET A 57 ALA A 155 SITE 2 AC5 8 NAG A1502 HOH A2725 HOH A2726 HOH A2727 SITE 1 AC6 12 ARG A 22 HIS A 153 LEU A 154 ALA A 155 SITE 2 AC6 12 VAL A 158 NAG A1501 HOH A2317 HOH A2728 SITE 3 AC6 12 HOH A2729 HOH A2730 HOH A2731 HOH A2733 SITE 1 AC7 10 THR A 289 SER A 382 ASN A 433 NAG A1504 SITE 2 AC7 10 HOH A2654 HOH A2734 HOH A2735 HOH A2736 SITE 3 AC7 10 HOH A2737 HOH A2739 SITE 1 AC8 5 ALA A 324 ASN A 326 NAG A1503 HOH A2740 SITE 2 AC8 5 HOH A2741 CRYST1 56.382 86.128 152.645 90.00 90.00 90.00 P 21 21 21 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 0.017736 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011611 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006551 0.00000