HEADER OXIDOREDUCTASE 22-JUN-20 6XJ0 TITLE CRYSTAL STRUCTURE OF MULTI-COPPER OXIDASE FROM PEDIOCOCCUS PENTOSACEUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTICOPPER OXIDASE MCO; COMPND 3 CHAIN: A; COMPND 4 EC: 1.-.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PEDIOCOCCUS PENTOSACEUS; SOURCE 3 ORGANISM_TAXID: 1255; SOURCE 4 GENE: MCO, NCTC8066_01952; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, LACCASE, COPPER OXIDASE, ACOUSTIC DROPLET EJECTION, KEYWDS 2 LIGNIN, COMBINATORIAL CRYSTALLIZATION EXPDTA X-RAY DIFFRACTION AUTHOR I.PARDO,A.S.SOARES,R.COLLINS,S.H.PARTOWMAH,E.A.COLER REVDAT 2 12-MAY-21 6XJ0 1 JRNL REVDAT 1 10-MAR-21 6XJ0 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. 2.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 110.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 28375 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1483 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2027 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4032 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 443 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.27000 REMARK 3 B22 (A**2) : 0.27000 REMARK 3 B33 (A**2) : -0.86000 REMARK 3 B12 (A**2) : 0.13000 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): 0.287 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.212 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.168 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.312 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4177 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3840 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5678 ; 1.856 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8870 ; 0.993 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 509 ; 7.537 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 200 ;36.751 ;24.350 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 655 ;15.722 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;19.233 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 604 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4737 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 956 ; 0.002 ; 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): 2036 ; 2.057 ; 2.721 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2035 ; 2.058 ; 2.719 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2545 ; 3.146 ; 4.072 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2546 ; 3.146 ; 4.075 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2141 ; 2.957 ; 3.024 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2139 ; 2.951 ; 3.025 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3132 ; 4.759 ; 4.394 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4863 ; 7.754 ;22.294 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4688 ; 7.445 ;22.083 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 REMARK 4 REMARK 4 6XJ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000247081. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9202 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29876 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.340 REMARK 200 RESOLUTION RANGE LOW (A) : 110.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.730 REMARK 200 R MERGE (I) : 0.33500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.70700 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: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: FLAT PLATE LIKE SINGLE CRYSTALS FORMED ON MYLAR SURFACE. REMARK 200 OTHER TESTED SURFACES (GLASS, KAPTON, POLY PROPYLENE, POLY REMARK 200 ETHYLENE, AND COC) YIELDED POORLY DIFFRACTING CRYSTALS, MICRO REMARK 200 CRYSTALS, OR POLY-CRYSTALS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION SCREENING ACCOMPLISHED REMARK 280 USING COMBINATORIAL CRYSTALLIZATION STRATEGY. SEPARATE LIBRARIES REMARK 280 OF PRECIPITANTS, BUFFERS, AND ADDITIVES WERE COMBINATORIALLY REMARK 280 COMBINED WITH PROTEIN (11 MG/ML PROTEIN IN 10 MM TRIS-HCL PH 7.0) REMARK 280 IN SITU ON THE CRYSTALLIZATION PLATE. FINAL CONCENTRATIONS OF REMARK 280 MOTHER LIQUOR: BUFFER: 83 MM SODIUM CITRATE PH 4.0 ADDITIVES: REMARK 280 670 MM LITHIUM SULFATE, 8 MM L-GLUTAMINE, 8 MM L-ASPARTIC ACID, REMARK 280 8 MM GLYCINE, 8 MM TRANS-4-HYDROXY-L-PROLINE. RESERVOIR SOLUTION: REMARK 280 PRECIPITANT: 2 M LITHIUM SULFATE CRYSTALS ONLY GROW ON MYLAR REMARK 280 SURFACE (MANY SURFACES WERE TESTED)., VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.18000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.09000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.09000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.18000 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 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 1046 O HOH A 1063 1.66 REMARK 500 O HOH A 989 O HOH A 1035 1.70 REMARK 500 O HOH A 1035 O HOH A 1103 1.96 REMARK 500 O HOH A 954 O HOH A 1102 1.98 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 ASP A 171 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 180 NE - CZ - NH2 ANGL. DEV. = -3.7 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 ASN A 75 16.87 55.87 REMARK 500 LEU A 79 -123.54 58.65 REMARK 500 ARG A 180 14.45 -151.81 REMARK 500 HIS A 197 -161.68 -114.43 REMARK 500 ARG A 245 -27.00 -144.47 REMARK 500 ALA A 282 -8.19 77.83 REMARK 500 ASP A 305 -132.92 56.87 REMARK 500 THR A 322 124.40 5.42 REMARK 500 PHE A 329 136.84 -172.99 REMARK 500 ASP A 351 -129.99 49.50 REMARK 500 ALA A 386 -136.02 89.98 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 ASP A 385 ALA A 386 133.26 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 A1142 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A1143 DISTANCE = 8.31 ANGSTROMS 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 602 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 106 NE2 REMARK 620 2 HIS A 394 NE2 169.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 C2O A 601 CU2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 108 ND1 REMARK 620 2 C2O A 601 O1 116.3 REMARK 620 3 HIS A 147 NE2 129.5 99.6 REMARK 620 4 HIS A 446 NE2 109.7 79.7 110.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 C2O A 601 CU3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 149 NE2 REMARK 620 2 C2O A 601 O1 102.5 REMARK 620 3 HIS A 396 NE2 98.4 127.8 REMARK 620 4 HIS A 444 NE2 119.6 103.9 106.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 603 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 391 ND1 REMARK 620 2 CYS A 445 SG 123.2 REMARK 620 3 HIS A 450 ND1 112.6 122.5 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 C2O A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 605 DBREF1 6XJ0 A 2 509 UNP A0A379CCN4_PEDPE DBREF2 6XJ0 A A0A379CCN4 2 509 SEQADV 6XJ0 ASN A 3 UNP A0A379CCN THR 3 CONFLICT SEQADV 6XJ0 ASN A 241 UNP A0A379CCN ASP 241 CONFLICT SEQADV 6XJ0 ALA A 253 UNP A0A379CCN SER 253 CONFLICT SEQRES 1 A 508 LYS ASN TYR THR ASP TYR PHE PHE ASP GLU PRO ALA PHE SEQRES 2 A 508 ASP LEU HIS ASP GLY GLY TYR VAL PRO LEU GLU VAL SER SEQRES 3 A 508 ASP ALA PRO GLU LYS PRO LEU ASN VAL PRO PRO LEU LEU SEQRES 4 A 508 LYS PRO ASP LYS GLU THR ALA THR ASP VAL TYR TYR THR SEQRES 5 A 508 VAL THR ALA GLU ALA GLY GLU THR GLN LEU LEU PRO GLY SEQRES 6 A 508 ALA LYS THR LYS THR TRP GLY TYR ASN THR SER LEU LEU SEQRES 7 A 508 GLY GLN THR ILE VAL TYR ARG ARG GLY GLN HIS THR HIS SEQRES 8 A 508 VAL THR LEU LYS ASN THR LEU PRO GLU LEU THR THR PHE SEQRES 9 A 508 HIS TRP HIS GLY ALA ASN VAL SER GLY PRO TYR VAL ASP SEQRES 10 A 508 GLY GLY CYS HIS ALA PRO VAL TYR PRO GLY GLU SER LYS SEQRES 11 A 508 HIS ILE ASP PHE THR LEU GLU GLN PRO ALA THR THR LEU SEQRES 12 A 508 TRP LEU HIS ALA HIS PRO CYS PRO SER THR ALA GLU GLN SEQRES 13 A 508 VAL TRP HIS GLY LEU ALA ALA MET VAL ILE VAL LYS ASP SEQRES 14 A 508 ASP HIS GLU ALA SER LEU PRO LEU PRO ARG ASN TYR GLY SEQRES 15 A 508 VAL ASP ASP ILE PRO VAL ILE LEU GLN ASP ARG ARG PHE SEQRES 16 A 508 HIS GLU ASN ASN GLN TRP ASP TYR ARG ALA ASP TYR ASP SEQRES 17 A 508 PRO ASP GLY VAL ALA GLY PRO THR ALA MET ILE ASN GLY SEQRES 18 A 508 THR ILE ASN PRO TYR PHE ASP VAL THR THR GLN LYS VAL SEQRES 19 A 508 ARG LEU ARG PHE LEU ASN GLY ALA ASN ARG ARG GLU TRP SEQRES 20 A 508 ARG LEU HIS PHE ALA ASP ASP LEU PRO PHE THR GLN ILE SEQRES 21 A 508 GLY GLY ASP GLY SER LEU LEU PRO GLU PRO VAL LYS PHE SEQRES 22 A 508 THR HIS LEU MET LEU THR CYS ALA GLU ARG ALA GLU VAL SEQRES 23 A 508 ILE VAL ASP PHE GLY GLN TYR HIS GLU GLY ASP GLU VAL SEQRES 24 A 508 THR LEU TYR THR ASP ASP VAL PRO LEU LEU LYS PHE ARG SEQRES 25 A 508 ILE HIS ALA PHE LYS PRO ASP GLN THR THR LEU PRO ASP SEQRES 26 A 508 LYS LEU PHE ASP VAL LYS ALA PRO VAL VAL ASP PRO ALA SEQRES 27 A 508 LEU PRO VAL ARG HIS VAL VAL MET GLN GLY MET ASP GLU SEQRES 28 A 508 GLY VAL ALA ILE ASP GLY LYS LYS PHE ALA MET GLN ARG SEQRES 29 A 508 ILE ASP ALA THR GLN PRO ILE GLY LYS ALA GLN TYR TRP SEQRES 30 A 508 ASP VAL THR ASN SER ASN ASP ALA PRO GLY MET VAL HIS SEQRES 31 A 508 PRO PHE HIS VAL HIS GLY THR GLN PHE LEU VAL LEU SER SEQRES 32 A 508 ARG ASN GLY HIS ALA PRO TYR PRO ASN GLU HIS GLY PHE SEQRES 33 A 508 LYS ASP THR ILE GLY VAL ASN PRO GLY GLU THR VAL ARG SEQRES 34 A 508 LEU LEU VAL ARG PHE ASP LEU PRO GLY VAL TYR MET TYR SEQRES 35 A 508 HIS CYS HIS ILE ILE GLU HIS GLU ASP GLY GLY MET MET SEQRES 36 A 508 ALA GLN ILE GLU THR PHE ASP PRO ALA LYS PRO LYS GLN SEQRES 37 A 508 GLU TYR LYS LEU MET ASP MET ASP THR LEU MET MET ALA SEQRES 38 A 508 LEU ALA LYS GLU ARG GLY VAL LYS PRO SER GLU ILE TRP SEQRES 39 A 508 MET GLY GLY MET GLN SER TYR GLU LYS MET GLY MET LYS SEQRES 40 A 508 MET HET C2O A 601 3 HET CU A 602 1 HET CU A 603 1 HET CL A 604 1 HET CL A 605 1 HETNAM C2O CU-O-CU LINKAGE HETNAM CU COPPER (II) ION HETNAM CL CHLORIDE ION FORMUL 2 C2O CU2 O FORMUL 3 CU 2(CU 2+) FORMUL 5 CL 2(CL 1-) FORMUL 7 HOH *443(H2 O) HELIX 1 AA1 ASP A 10 ASP A 18 5 9 HELIX 2 AA2 SER A 153 GLY A 161 1 9 HELIX 3 AA3 ASP A 170 SER A 175 1 6 HELIX 4 AA4 HIS A 197 GLN A 201 5 5 HELIX 5 AA5 ASP A 203 TYR A 208 1 6 HELIX 6 AA6 ASP A 254 LEU A 256 5 3 HELIX 7 AA7 MET A 350 VAL A 354 5 5 HELIX 8 AA8 ILE A 447 GLY A 453 1 7 HELIX 9 AA9 ASP A 475 GLY A 488 1 14 HELIX 10 AB1 LYS A 490 ILE A 494 5 5 HELIX 11 AB2 GLY A 498 MET A 505 1 8 SHEET 1 AA1 7 ASN A 3 TYR A 4 0 SHEET 2 AA1 7 LEU A 267 PHE A 274 1 O LYS A 273 N TYR A 4 SHEET 3 AA1 7 PHE A 258 GLY A 262 -1 N PHE A 258 O PHE A 274 SHEET 4 AA1 7 ARG A 284 ASP A 290 -1 O GLU A 286 N ILE A 261 SHEET 5 AA1 7 LYS A 234 ASN A 241 -1 N VAL A 235 O VAL A 289 SHEET 6 AA1 7 ASP A 186 ARG A 194 1 N LEU A 191 O LEU A 240 SHEET 7 AA1 7 THR A 217 ILE A 220 -1 O MET A 219 N GLN A 192 SHEET 1 AA2 6 LYS A 32 PRO A 33 0 SHEET 2 AA2 6 PRO A 226 VAL A 230 1 O TYR A 227 N LYS A 32 SHEET 3 AA2 6 VAL A 307 ILE A 314 1 O LYS A 311 N PHE A 228 SHEET 4 AA2 6 GLU A 299 THR A 304 -1 N VAL A 300 O PHE A 312 SHEET 5 AA2 6 TRP A 248 PHE A 252 -1 N HIS A 251 O TYR A 303 SHEET 6 AA2 6 LEU A 277 LEU A 279 -1 O LEU A 277 N LEU A 250 SHEET 1 AA3 4 LYS A 44 GLU A 45 0 SHEET 2 AA3 4 ASP A 49 THR A 61 -1 O TYR A 51 N LYS A 44 SHEET 3 AA3 4 THR A 69 TYR A 74 -1 O THR A 71 N GLY A 59 SHEET 4 AA3 4 LEU A 79 GLY A 80 1 O LEU A 79 N TYR A 74 SHEET 1 AA4 4 LYS A 44 GLU A 45 0 SHEET 2 AA4 4 ASP A 49 THR A 61 -1 O TYR A 51 N LYS A 44 SHEET 3 AA4 4 HIS A 90 ASN A 97 1 O THR A 94 N TYR A 52 SHEET 4 AA4 4 SER A 130 THR A 136 -1 O LYS A 131 N LEU A 95 SHEET 1 AA5 4 ILE A 83 ARG A 86 0 SHEET 2 AA5 4 ALA A 163 LYS A 169 1 O ILE A 167 N ILE A 83 SHEET 3 AA5 4 THR A 142 HIS A 147 -1 N THR A 142 O VAL A 168 SHEET 4 AA5 4 HIS A 106 HIS A 108 -1 N HIS A 106 O HIS A 147 SHEET 1 AA6 6 ALA A 355 ILE A 356 0 SHEET 2 AA6 6 ARG A 343 GLN A 348 -1 N GLN A 348 O ALA A 355 SHEET 3 AA6 6 GLN A 376 ASN A 382 1 O ASP A 379 N ARG A 343 SHEET 4 AA6 6 THR A 428 VAL A 433 -1 O VAL A 429 N VAL A 380 SHEET 5 AA6 6 PHE A 400 ARG A 405 -1 N LEU A 403 O ARG A 430 SHEET 6 AA6 6 PHE A 417 LYS A 418 -1 O LYS A 418 N PHE A 400 SHEET 1 AA7 5 ALA A 368 PRO A 371 0 SHEET 2 AA7 5 MET A 456 PHE A 462 1 O GLU A 460 N ALA A 368 SHEET 3 AA7 5 GLY A 439 CYS A 445 -1 N GLY A 439 O THR A 461 SHEET 4 AA7 5 HIS A 391 VAL A 395 -1 N HIS A 394 O HIS A 444 SHEET 5 AA7 5 THR A 420 VAL A 423 -1 O ILE A 421 N PHE A 393 SSBOND 1 CYS A 121 CYS A 151 1555 1555 2.04 LINK NE2 HIS A 106 CU CU A 602 1555 1555 2.03 LINK ND1 HIS A 108 CU2 C2O A 601 1555 1555 2.08 LINK NE2 HIS A 147 CU2 C2O A 601 1555 1555 2.05 LINK NE2 HIS A 149 CU3 C2O A 601 1555 1555 2.11 LINK ND1 HIS A 391 CU CU A 603 1555 1555 2.03 LINK NE2 HIS A 394 CU CU A 602 1555 1555 2.04 LINK NE2 HIS A 396 CU3 C2O A 601 1555 1555 2.09 LINK NE2 HIS A 444 CU3 C2O A 601 1555 1555 2.11 LINK SG CYS A 445 CU CU A 603 1555 1555 2.22 LINK NE2 HIS A 446 CU2 C2O A 601 1555 1555 2.13 LINK ND1 HIS A 450 CU CU A 603 1555 1555 2.09 CISPEP 1 GLY A 114 PRO A 115 0 1.71 CISPEP 2 CYS A 151 PRO A 152 0 -5.74 CISPEP 3 PRO A 152 SER A 153 0 -12.67 SITE 1 AC1 8 HIS A 108 HIS A 147 HIS A 149 HIS A 394 SITE 2 AC1 8 HIS A 396 HIS A 444 HIS A 446 CU A 602 SITE 1 AC2 6 HIS A 106 HIS A 108 HIS A 394 HIS A 396 SITE 2 AC2 6 C2O A 601 HOH A 844 SITE 1 AC3 4 HIS A 391 CYS A 445 HIS A 450 MET A 455 SITE 1 AC4 2 ARG A 487 TRP A 495 SITE 1 AC5 2 HOH A1041 HOH A1116 CRYST1 127.370 127.370 75.270 90.00 90.00 120.00 P 32 2 1 6 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 0.007851 0.004533 0.000000 0.00000 SCALE2 0.000000 0.009066 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013286 0.00000