HEADER OXIDOREDUCTASE 09-MAY-20 6Z0J TITLE CRYSTAL STRUCTURE OF LACCASE FROM PEDIOCOCCUS ACIDILACTICI PA5930 TITLE 2 (TRIS-HCL PH 8.5) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE MULTICOPPER OXIDASE MCO; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PEDIOCOCCUS ACIDILACTICI 7_4; SOURCE 3 ORGANISM_TAXID: 563194; SOURCE 4 GENE: HMPREF9024_01129; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS LACCASE, MULTICOPPER OXIDASE, LACTIC ACID BACTERIA, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.CASINO,J.HUESA,I.PARDO REVDAT 4 24-JAN-24 6Z0J 1 REMARK REVDAT 3 12-MAY-21 6Z0J 1 JRNL REVDAT 2 17-MAR-21 6Z0J 1 JRNL REVDAT 1 10-MAR-21 6Z0J 0 JRNL AUTH I.OLMEDA,P.CASINO,R.E.COLLINS,R.SENDRA,S.CALLEJON,J.HUESA, JRNL AUTH 2 A.S.SOARES,S.FERRER,I.PARDO JRNL TITL STRUCTURAL ANALYSIS AND BIOCHEMICAL PROPERTIES OF LACCASE JRNL TITL 2 ENZYMES FROM TWO PEDIOCOCCUS SPECIES. JRNL REF MICROB BIOTECHNOL V. 14 1026 2021 JRNL REFN ISSN 1751-7915 JRNL PMID 33635570 JRNL DOI 10.1111/1751-7915.13751 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16257 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) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 865 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1184 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.4040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3697 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.31000 REMARK 3 B22 (A**2) : -2.64000 REMARK 3 B33 (A**2) : 6.95000 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): 0.969 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.327 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.325 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.971 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3801 ; 0.003 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3386 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5177 ; 1.264 ; 1.647 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7885 ; 1.095 ; 1.574 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 460 ; 7.175 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 215 ;33.279 ;23.209 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 611 ;16.964 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;15.798 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 485 ; 0.044 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4289 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 783 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6Z0J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292108647. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97925 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17180 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 94.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.14800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.90400 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: PHASER REMARK 200 STARTING MODEL: 3ZDW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG1000 AND 0.1M TRIS-HCL PH 8.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K 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 25.89850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.78200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.14700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.78200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.89850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.14700 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 TOTAL BURIED SURFACE AREA: 380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 PRO A 462 REMARK 465 ASP A 463 REMARK 465 HIS A 464 REMARK 465 PRO A 465 REMARK 465 ILE A 466 REMARK 465 GLU A 467 REMARK 465 TYR A 468 REMARK 465 HIS A 469 REMARK 465 LEU A 470 REMARK 465 MET A 471 REMARK 465 PRO A 472 REMARK 465 MET A 473 REMARK 465 ASN A 474 REMARK 465 HIS A 475 REMARK 465 LYS A 476 REMARK 465 MET A 477 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 ASP A 461 CG OD1 OD2 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 NH2 ARG A 192 O HOH A 601 2.16 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 PRO A 150 N - CA - CB ANGL. DEV. = -7.8 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 LEU A 6 -5.30 70.85 REMARK 500 ARG A 42 139.83 -170.38 REMARK 500 ASN A 46 -15.04 83.35 REMARK 500 ILE A 61 -64.10 -109.03 REMARK 500 LEU A 77 -130.11 51.97 REMARK 500 ALA A 121 65.59 -111.07 REMARK 500 HIS A 147 46.37 -145.90 REMARK 500 ARG A 179 99.92 -65.62 REMARK 500 ASP A 200 86.65 -155.55 REMARK 500 ARG A 242 -41.55 -138.43 REMARK 500 ALA A 279 -9.37 81.80 REMARK 500 ASP A 302 -128.92 56.97 REMARK 500 ASP A 348 -120.61 50.24 REMARK 500 ASP A 370 9.99 58.94 REMARK 500 ASN A 381 153.04 -49.54 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 CYS A 149 PRO A 150 -30.30 REMARK 500 REMARK 500 REMARK: NULL 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 A 504 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 104 NE2 REMARK 620 2 HIS A 392 NE2 159.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 502 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 106 ND1 REMARK 620 2 HIS A 145 NE2 137.2 REMARK 620 3 HIS A 444 NE2 106.5 115.3 REMARK 620 4 HOH A 639 O 108.9 86.0 82.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 503 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 147 NE2 REMARK 620 2 HIS A 394 NE2 108.8 REMARK 620 3 HIS A 442 NE2 108.8 98.9 REMARK 620 4 HOH A 639 O 116.0 118.4 104.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 389 ND1 REMARK 620 2 CYS A 443 SG 117.3 REMARK 620 3 HIS A 448 ND1 106.9 113.2 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 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 504 DBREF 6Z0J A 1 477 UNP D2EK17 D2EK17_PEDAC 1 477 SEQADV 6Z0J ILE A 232 UNP D2EK17 VAL 232 CONFLICT SEQADV 6Z0J ARG A 430 UNP D2EK17 LYS 430 CONFLICT SEQRES 1 A 477 MET ILE THR LYS TYR LEU TYR ASP GLU ASN ALA TYR ASP SEQRES 2 A 477 TYR HIS ASP GLY GLY TYR ARG PRO LEU LYS LYS ALA PRO SEQRES 3 A 477 GLY GLU GLU HIS PRO LEU ASN VAL PRO ALA PHE LEU LYS SEQRES 4 A 477 PRO ASP ARG ILE GLU GLY ASN GLU ILE TYR TYR THR VAL SEQRES 5 A 477 THR ALA GLN ALA GLY GLU THR LYS ILE LEU PRO GLY LYS SEQRES 6 A 477 PRO THR HIS THR TRP GLY TYR ASN GLY SER ILE LEU GLY SEQRES 7 A 477 PRO ALA ILE GLN PHE GLU THR GLY LYS THR TYR HIS VAL SEQRES 8 A 477 THR LEU LYS ASN GLU LEU ASP GLU VAL THR THR PHE HIS SEQRES 9 A 477 TRP HIS GLY LEU ASN ILE VAL GLY PRO TYR GLU ASP GLY SEQRES 10 A 477 GLY PRO HIS ALA PRO VAL TYR PRO HIS GLY GLU ARG LYS SEQRES 11 A 477 ILE THR PHE THR VAL ASP GLN PRO ALA ALA ASN ILE TRP SEQRES 12 A 477 LEU HIS PRO HIS PRO CYS PRO GLU THR ALA ARG GLN VAL SEQRES 13 A 477 TRP ASN GLY LEU ALA ALA PRO VAL ILE ILE THR ASP GLY SEQRES 14 A 477 HIS GLU GLN SER LEU LYS LEU PRO ARG ARG TRP GLY VAL SEQRES 15 A 477 ASN ASP PHE PRO VAL VAL LEU GLN ASP ARG SER TYR HIS SEQRES 16 A 477 ASP ASN GLN LEU ASP TYR LYS ALA ASP TYR ASP VAL ASP SEQRES 17 A 477 GLY THR LEU GLY ASP TYR ALA LEU VAL ASN GLY THR VAL SEQRES 18 A 477 ASN PRO VAL VAL ASN VAL THR LYS PRO ILE ILE ARG LEU SEQRES 19 A 477 ARG PHE LEU ASN GLY SER ASN ARG ARG GLU TRP ARG LEU SEQRES 20 A 477 HIS PHE ALA ASP TYR HIS PRO PHE THR GLN ILE GLY SER SEQRES 21 A 477 ASP GLY GLY LEU LEU PRO GLU ALA VAL GLU MET ASP ARG SEQRES 22 A 477 ILE MET LEU THR CYS ALA GLU ARG ALA ASP VAL LEU VAL SEQRES 23 A 477 ASN PHE SER ASP TYR GLN PRO GLY GLN GLU VAL ILE LEU SEQRES 24 A 477 GLN THR ASP ASP PHE ASN LEU ILE LYS PHE LYS ILE GLY SEQRES 25 A 477 ASP ILE LYS LYS GLU ASN MET LEU LEU PRO SER PRO LEU SEQRES 26 A 477 ALA GLU ILE PRO ALA LEU SER VAL ASP GLU ASN THR PRO SEQRES 27 A 477 VAL PHE LYS THR VAL MET SER GLY MET ASP ASP GLN VAL SEQRES 28 A 477 ARG LEU ASP GLY LYS LEU PHE ASP MET GLN ARG ILE ASP SEQRES 29 A 477 THR ARG GLN GLN VAL ASP GLN THR GLN ILE TRP GLU VAL SEQRES 30 A 477 SER ASN THR ASN ASP MET GLU GLY GLY MET ILE HIS PRO SEQRES 31 A 477 PHE HIS ILE HIS GLY CYS GLN PHE GLN LEU ILE ASP ARG SEQRES 32 A 477 ASN GLY HIS ALA VAL ASN PRO ASN GLU HIS GLY TRP LYS SEQRES 33 A 477 ASP THR ILE GLY VAL ASN PRO ASN GLU THR VAL ARG ILE SEQRES 34 A 477 ARG VAL LYS PHE THR LYS LEU GLY ILE PHE MET TYR HIS SEQRES 35 A 477 CYS HIS ILE LEU GLU HIS GLU ASP THR GLY MET MET ALA SEQRES 36 A 477 GLN ILE GLU ILE PHE ASP PRO ASP HIS PRO ILE GLU TYR SEQRES 37 A 477 HIS LEU MET PRO MET ASN HIS LYS MET HET CU A 501 1 HET CU A 502 1 HET CU A 503 1 HET CU A 504 1 HETNAM CU COPPER (II) ION FORMUL 2 CU 4(CU 2+) FORMUL 6 HOH *50(H2 O) HELIX 1 AA1 ASP A 8 ASP A 16 5 9 HELIX 2 AA2 GLU A 151 ASN A 158 1 8 HELIX 3 AA3 ASP A 168 LEU A 174 1 7 HELIX 4 AA4 ASP A 200 TYR A 205 1 6 HELIX 5 AA5 SER A 289 TYR A 291 5 3 HELIX 6 AA6 MET A 347 VAL A 351 5 5 HELIX 7 AA7 ILE A 445 GLY A 452 1 8 SHEET 1 AA1 6 HIS A 30 PRO A 31 0 SHEET 2 AA1 6 PRO A 223 VAL A 227 1 O VAL A 224 N HIS A 30 SHEET 3 AA1 6 PHE A 304 ILE A 311 1 O LYS A 308 N VAL A 225 SHEET 4 AA1 6 GLU A 296 THR A 301 -1 N VAL A 297 O PHE A 309 SHEET 5 AA1 6 TRP A 245 PHE A 249 -1 N HIS A 248 O GLN A 300 SHEET 6 AA1 6 ILE A 274 LEU A 276 -1 O LEU A 276 N TRP A 245 SHEET 1 AA2 3 ARG A 42 GLU A 44 0 SHEET 2 AA2 3 GLU A 47 THR A 59 -1 O GLU A 47 N GLU A 44 SHEET 3 AA2 3 THR A 67 TYR A 72 -1 O THR A 67 N THR A 59 SHEET 1 AA3 4 ARG A 42 GLU A 44 0 SHEET 2 AA3 4 GLU A 47 THR A 59 -1 O GLU A 47 N GLU A 44 SHEET 3 AA3 4 THR A 88 ASN A 95 1 O THR A 88 N ILE A 48 SHEET 4 AA3 4 GLY A 127 THR A 134 -1 O ARG A 129 N LEU A 93 SHEET 1 AA4 4 ILE A 81 GLU A 84 0 SHEET 2 AA4 4 ALA A 162 THR A 167 1 O ILE A 165 N PHE A 83 SHEET 3 AA4 4 ALA A 140 HIS A 145 -1 N ILE A 142 O VAL A 164 SHEET 4 AA4 4 HIS A 104 HIS A 106 -1 N HIS A 104 O HIS A 145 SHEET 1 AA5 6 TYR A 214 VAL A 217 0 SHEET 2 AA5 6 ASP A 184 ARG A 192 -1 N GLN A 190 O LEU A 216 SHEET 3 AA5 6 ILE A 231 ASN A 238 1 O LEU A 237 N LEU A 189 SHEET 4 AA5 6 ARG A 281 ASN A 287 -1 O VAL A 284 N LEU A 234 SHEET 5 AA5 6 PHE A 255 SER A 260 -1 N ILE A 258 O ASP A 283 SHEET 6 AA5 6 GLY A 263 MET A 271 -1 O VAL A 269 N GLN A 257 SHEET 1 AA6 5 ARG A 352 LEU A 353 0 SHEET 2 AA6 5 VAL A 339 SER A 345 -1 N SER A 345 O ARG A 352 SHEET 3 AA6 5 GLN A 373 ASN A 379 1 O SER A 378 N MET A 344 SHEET 4 AA6 5 GLU A 425 VAL A 431 -1 O ILE A 429 N TRP A 375 SHEET 5 AA6 5 GLN A 399 ARG A 403 -1 N ILE A 401 O ARG A 428 SHEET 1 AA7 5 THR A 365 GLN A 368 0 SHEET 2 AA7 5 MET A 454 PHE A 460 1 O GLU A 458 N GLN A 367 SHEET 3 AA7 5 GLY A 437 CYS A 443 -1 N PHE A 439 O ILE A 457 SHEET 4 AA7 5 HIS A 389 ILE A 393 -1 N HIS A 392 O HIS A 442 SHEET 5 AA7 5 THR A 418 VAL A 421 -1 O ILE A 419 N PHE A 391 LINK NE2 HIS A 104 CU CU A 504 1555 1555 2.19 LINK ND1 HIS A 106 CU CU A 502 1555 1555 2.10 LINK NE2 HIS A 145 CU CU A 502 1555 1555 2.15 LINK NE2 HIS A 147 CU CU A 503 1555 1555 2.14 LINK ND1 HIS A 389 CU CU A 501 1555 1555 2.59 LINK NE2 HIS A 392 CU CU A 504 1555 1555 2.00 LINK NE2 HIS A 394 CU CU A 503 1555 1555 2.11 LINK NE2 HIS A 442 CU CU A 503 1555 1555 2.28 LINK SG CYS A 443 CU CU A 501 1555 1555 2.31 LINK NE2 HIS A 444 CU CU A 502 1555 1555 2.17 LINK ND1 HIS A 448 CU CU A 501 1555 1555 2.19 LINK CU CU A 502 O HOH A 639 1555 1555 2.27 LINK CU CU A 503 O HOH A 639 1555 1555 2.32 CISPEP 1 GLY A 112 PRO A 113 0 -1.53 CISPEP 2 SER A 323 PRO A 324 0 -0.92 SITE 1 AC1 4 HIS A 389 CYS A 443 HIS A 448 MET A 453 SITE 1 AC2 5 HIS A 106 HIS A 145 HIS A 444 CU A 504 SITE 2 AC2 5 HOH A 639 SITE 1 AC3 5 HIS A 147 HIS A 394 HIS A 442 CU A 504 SITE 2 AC3 5 HOH A 639 SITE 1 AC4 8 HIS A 104 HIS A 106 HIS A 392 HIS A 394 SITE 2 AC4 8 CU A 502 CU A 503 HOH A 639 HOH A 640 CRYST1 51.797 94.294 97.564 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 0.019306 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010250 0.00000