HEADER OXIDOREDUCTASE 31-JAN-20 6VOX TITLE CRYSTAL STRUCTURE OF MULTI-COPPER OXIDASE FROM PSEUDOMONAS PARAFULVA CAVEAT 6VOX RESIDUES LEU A 395 AND HIS A 396 THAT ARE NEXT TO EACH OTHER CAVEAT 2 6VOX IN THE SAMPLE SEQUENCE ARE NOT PROPERLY LINKED: DISTANCE CAVEAT 3 6VOX BETWEEN C AND N IS 2.23 RESIDUES HIS A 396 AND GLY A 397 CAVEAT 4 6VOX THAT ARE NEXT TO EACH OTHER IN THE SAMPLE SEQUENCE ARE NOT CAVEAT 5 6VOX PROPERLY LINKED: DISTANCE BETWEEN C AND N IS 2.83 RESIDUES CAVEAT 6 6VOX PHE A 441 AND HIS A 442 THAT ARE NEXT TO EACH OTHER IN THE CAVEAT 7 6VOX SAMPLE SEQUENCE ARE NOT PROPERLY LINKED: DISTANCE BETWEEN C CAVEAT 8 6VOX AND N IS 2.25 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER OXIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PARAFULVA; SOURCE 3 ORGANISM_TAXID: 157782; SOURCE 4 GENE: NJ69_01745; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, LACCASE, COPPER OXIDASE, ACOUSTIC DROPLET EJECTION, KEYWDS 2 LIGNIN EXPDTA X-RAY DIFFRACTION AUTHOR S.H.PARTOWMAH,E.A.COLER,A.S.SOARES,R.E.COLLINS REVDAT 2 11-OCT-23 6VOX 1 REMARK REVDAT 1 03-FEB-21 6VOX 0 JRNL AUTH S.PARTOWMAH,E.A.COLER,A.S.SOARES,R.E.COLLINS JRNL TITL CRYSTAL STRUCTURE OF MULTI-COPPER OXIDASE FROM PSEUDOMONAS JRNL TITL 2 PARAFULVA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 10435 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) : 0.258 REMARK 3 R VALUE (WORKING SET) : 0.258 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 215 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) : 3.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 626 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.4480 REMARK 3 BIN FREE R VALUE SET COUNT : 12 REMARK 3 BIN FREE R VALUE : 0.4910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3198 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 195.2 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.23000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : -0.74000 REMARK 3 B12 (A**2) : 0.11000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.596 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.600 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 51.885 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3288 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3100 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4475 ; 1.984 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7128 ; 1.202 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 401 ;12.096 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 147 ;38.621 ;23.265 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 516 ;22.836 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;17.043 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 486 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3685 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 757 ; 0.003 ; 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): 1622 ;16.925 ;18.978 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1621 ;16.926 ;18.978 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2017 ;27.386 ;28.393 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2018 ;27.379 ;28.392 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1666 ;14.191 ;20.355 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1664 ;14.148 ;20.369 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2457 ;24.129 ;30.038 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 13556 ;40.447 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 13553 ;40.449 ; 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 : NULL 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 6VOX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000246788. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 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 EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10690 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.800 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 (%) : 92.3 REMARK 200 DATA REDUNDANCY : 29.33 REMARK 200 R MERGE (I) : 0.29000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.57800 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: 6VOW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 78.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZED IN PLASTIC SITTING DROP REMARK 280 TRAYS, 30 NL OF PROTEIN (CONCENTRATION 10 MG/ML) COMBINED WITH REMARK 280 30 NL PRECIPITANT: 0.0425 M BICINE PH 9.0 0.0425 M SODIUM REMARK 280 CHLORIDE 8.5% V/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 550 7.5% REMARK 280 V/V GLYCEROL SOLUTION WAS EQUILIBRATED AGAINST A RESERVOIR OF 60% REMARK 280 PEG 3350., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 87.33333 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 43.66667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 87.33333 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 43.66667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 87.33333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 43.66667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 87.33333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 43.66667 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 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 ALA A 335 REMARK 465 GLY A 336 REMARK 465 LYS A 337 REMARK 465 VAL A 338 REMARK 465 SER A 339 REMARK 465 VAL A 340 REMARK 465 ASP A 341 REMARK 465 THR A 342 REMARK 465 ASP A 343 REMARK 465 ASN A 344 REMARK 465 GLY A 345 REMARK 465 ARG A 346 REMARK 465 THR A 361 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 41 CG OD1 OD2 REMARK 470 GLU A 43 CG CD OE1 OE2 REMARK 470 PHE A 330 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 331 CG OD1 ND2 REMARK 470 PHE A 332 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 333 CG CD OE1 OE2 REMARK 470 TRP A 334 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 334 CZ3 CH2 REMARK 470 TRP A 351 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 351 CZ3 CH2 REMARK 470 ARG A 368 CG CD NE CZ NH1 NH2 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 CE1 HIS A 442 SD MET A 449 2.12 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 LEU A 328 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 PHE A 332 N - CA - C ANGL. DEV. = 18.4 DEGREES REMARK 500 LEU A 350 N - CA - C ANGL. DEV. = 18.3 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 GLU A 43 -137.41 -86.10 REMARK 500 LEU A 44 114.46 126.64 REMARK 500 PRO A 48 87.95 -68.85 REMARK 500 GLU A 52 86.74 -66.41 REMARK 500 PHE A 57 -177.26 -175.20 REMARK 500 LYS A 58 -161.77 -76.84 REMARK 500 THR A 59 110.29 159.32 REMARK 500 PRO A 66 -169.21 -101.15 REMARK 500 SER A 67 43.77 32.01 REMARK 500 PRO A 69 107.54 -51.96 REMARK 500 TRP A 80 96.05 -39.49 REMARK 500 THR A 93 131.36 -171.44 REMARK 500 ILE A 100 131.02 -7.63 REMARK 500 ARG A 101 70.07 -116.04 REMARK 500 PRO A 103 128.01 -38.35 REMARK 500 GLU A 105 -48.64 -25.26 REMARK 500 TYR A 111 -41.94 115.77 REMARK 500 SER A 113 -94.44 -59.91 REMARK 500 TYR A 135 -166.22 -125.17 REMARK 500 HIS A 138 153.74 169.84 REMARK 500 SER A 142 48.27 24.05 REMARK 500 LEU A 155 89.45 -155.11 REMARK 500 GLU A 158 100.82 -50.26 REMARK 500 GLU A 159 119.69 -39.29 REMARK 500 PRO A 162 102.48 -55.68 REMARK 500 THR A 163 116.26 -37.33 REMARK 500 PRO A 186 151.37 -49.31 REMARK 500 ARG A 195 -143.98 -87.75 REMARK 500 ARG A 201 -58.44 -153.24 REMARK 500 ASN A 206 27.59 48.82 REMARK 500 GLU A 210 90.70 53.27 REMARK 500 VAL A 212 68.17 -117.35 REMARK 500 TYR A 247 -41.95 -132.20 REMARK 500 VAL A 254 -166.56 -163.96 REMARK 500 PRO A 258 -169.99 -107.32 REMARK 500 LEU A 259 -60.22 -10.01 REMARK 500 GLU A 260 179.28 65.25 REMARK 500 ASP A 261 -177.70 -62.09 REMARK 500 ILE A 271 101.64 -169.92 REMARK 500 PRO A 278 -171.42 -68.93 REMARK 500 ALA A 280 -161.63 -51.94 REMARK 500 GLU A 282 114.20 -34.44 REMARK 500 ARG A 292 90.97 -58.31 REMARK 500 SER A 302 47.00 -92.28 REMARK 500 ALA A 311 150.97 -47.64 REMARK 500 ALA A 318 69.91 -36.10 REMARK 500 PHE A 330 -116.00 137.92 REMARK 500 ASN A 331 163.46 76.13 REMARK 500 PHE A 332 128.94 83.94 REMARK 500 GLU A 333 -164.41 167.38 REMARK 500 REMARK 500 THIS ENTRY HAS 73 RAMACHANDRAN OUTLIERS. 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 PRO A 110 TYR A 111 146.02 REMARK 500 GLU A 279 ALA A 280 -148.61 REMARK 500 ASP A 321 LEU A 322 -148.37 REMARK 500 SER A 349 LEU A 350 -145.73 REMARK 500 LYS A 409 ILE A 410 -148.12 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 C2O A 501 CU3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 96 NE2 REMARK 620 2 C2O A 501 O1 94.7 REMARK 620 3 HIS A 140 NE2 121.4 90.4 REMARK 620 4 HIS A 396 NE2 97.9 128.5 122.9 REMARK 620 N 1 2 3 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 96 NE2 REMARK 620 2 HIS A 394 NE2 101.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 C2O A 501 CU2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 98 ND1 REMARK 620 2 C2O A 501 O1 108.2 REMARK 620 3 HIS A 138 NE2 98.6 131.0 REMARK 620 4 HIS A 444 NE2 128.9 89.3 104.9 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 391 ND1 REMARK 620 2 CYS A 443 SG 80.6 REMARK 620 3 HIS A 448 ND1 88.9 128.4 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 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6VOW RELATED DB: PDB REMARK 900 COPPER OXIDASE SOLVED DURING SAME PROJECT DBREF1 6VOX A 40 459 UNP A0A0A7JLK4_9PSED DBREF2 6VOX A A0A0A7JLK4 40 459 SEQRES 1 A 420 HIS ASP TYR GLU LEU ILE ALA ALA PRO LEU ASP VAL GLU SEQRES 2 A 420 LEU VAL PRO GLY PHE LYS THR GLU ALA TRP ALA PHE GLY SEQRES 3 A 420 PRO SER ALA PRO GLY THR GLU LEU ARG VAL ARG GLN GLY SEQRES 4 A 420 THR TRP LEU ARG VAL ARG PHE ILE ASN HIS LEU PRO VAL SEQRES 5 A 420 GLU THR THR ILE HIS TRP HIS GLY ILE ARG LEU PRO LEU SEQRES 6 A 420 GLU MET ASP GLY VAL PRO TYR VAL SER GLN LEU PRO VAL SEQRES 7 A 420 LYS PRO GLY GLU PHE PHE ASP TYR LYS PHE ARG VAL PRO SEQRES 8 A 420 ASP ALA GLY SER TYR TRP TYR HIS PRO HIS VAL SER SER SEQRES 9 A 420 SER GLU GLU LEU GLY ARG GLY LEU VAL GLY PRO LEU ILE SEQRES 10 A 420 VAL GLU GLU ARG GLU PRO THR GLY PHE LEU HIS GLU ARG SEQRES 11 A 420 THR LEU SER LEU LYS THR TRP HIS VAL ASP GLU GLN GLY SEQRES 12 A 420 ALA PHE MET PRO PHE SER VAL PRO ARG GLU ALA ALA ARG SEQRES 13 A 420 ASN GLY THR ALA GLY ARG LEU ILE THR ILE ASN GLY GLN SEQRES 14 A 420 ALA GLU SER VAL THR GLU LEU PRO ALA GLY GLN VAL VAL SEQRES 15 A 420 ARG VAL ARG LEU LEU ASN LEU ASP ASN THR TRP THR TYR SEQRES 16 A 420 ARG ILE ASN LEU LYS GLY ASN CYS GLU ALA LYS VAL TYR SEQRES 17 A 420 ALA LEU ASP GLY ASN PRO VAL THR PRO ARG PRO LEU GLU SEQRES 18 A 420 ASP GLU TYR TRP LEU GLY PRO GLY MET ARG ILE CYS LEU SEQRES 19 A 420 ALA ILE ARG ILE PRO GLU ALA GLY GLU GLU ILE SER LEU SEQRES 20 A 420 ARG ASP GLY PHE VAL ARG LEU GLY THR LEU ARG SER VAL SEQRES 21 A 420 ALA SER SER GLU ALA PRO GLY ASN TRP PRO LYS ALA LEU SEQRES 22 A 420 PRO PRO ASN PRO ILE ALA GLU PRO ASP LEU GLU LYS ALA SEQRES 23 A 420 GLU LYS LEU ASN PHE ASN PHE GLU TRP ALA GLY LYS VAL SEQRES 24 A 420 SER VAL ASP THR ASP ASN GLY ARG PRO PRO SER LEU TRP SEQRES 25 A 420 GLN ILE ASN GLY GLN ALA TRP ASP ILE THR ASP LYS THR SEQRES 26 A 420 CYS ALA ASP ARG PRO ILE ALA THR LEU LYS LYS GLY LYS SEQRES 27 A 420 SER TYR ILE PHE GLU LEU LYS ASN MET THR GLN TYR GLN SEQRES 28 A 420 HIS PRO ILE HIS LEU HIS GLY MET SER PHE LYS VAL ILE SEQRES 29 A 420 ALA SER ASN ARG HIS LYS ILE THR GLU PRO TRP PHE THR SEQRES 30 A 420 ASP THR TYR LEU LEU GLY ARG ASN GLU ARG ALA GLN VAL SEQRES 31 A 420 ALA LEU VAL ALA ASP ASN PRO GLY THR TRP MET PHE HIS SEQRES 32 A 420 CYS HIS VAL ILE ASP HIS MET GLU THR GLY LEU MET ALA SEQRES 33 A 420 ALA ILE ALA VAL HET C2O A 501 3 HET CU A 502 1 HET CU A 503 1 HETNAM C2O CU-O-CU LINKAGE HETNAM CU COPPER (II) ION FORMUL 2 C2O CU2 O FORMUL 3 CU 2(CU 2+) HELIX 1 AA1 PRO A 103 GLY A 108 5 6 HELIX 2 AA2 SER A 142 ARG A 149 1 8 HELIX 3 AA3 VAL A 189 ALA A 194 1 6 HELIX 4 AA4 VAL A 445 THR A 451 1 7 SHEET 1 AA1 3 ASP A 41 TYR A 42 0 SHEET 2 AA1 3 ARG A 82 ARG A 84 1 O ARG A 82 N TYR A 42 SHEET 3 AA1 3 ASP A 124 TYR A 125 -1 O TYR A 125 N VAL A 83 SHEET 1 AA2 4 ARG A 74 ARG A 76 0 SHEET 2 AA2 4 GLY A 153 GLU A 158 1 O GLU A 158 N VAL A 75 SHEET 3 AA2 4 TYR A 135 HIS A 138 -1 N TYR A 137 O GLY A 153 SHEET 4 AA2 4 HIS A 96 HIS A 98 -1 N HIS A 96 O HIS A 138 SHEET 1 AA3 4 LEU A 202 ILE A 205 0 SHEET 2 AA3 4 HIS A 167 TRP A 176 -1 N LYS A 174 O THR A 204 SHEET 3 AA3 4 VAL A 221 ASN A 227 1 O LEU A 226 N LEU A 173 SHEET 4 AA3 4 ARG A 270 ILE A 271 -1 O ILE A 271 N LEU A 225 SHEET 1 AA4 4 TYR A 263 LEU A 265 0 SHEET 2 AA4 4 TYR A 234 LEU A 238 -1 N TYR A 234 O LEU A 265 SHEET 3 AA4 4 GLY A 281 ASP A 288 -1 O ARG A 287 N ASN A 237 SHEET 4 AA4 4 VAL A 291 SER A 298 -1 O VAL A 291 N ASP A 288 SHEET 1 AA5 2 LYS A 245 VAL A 246 0 SHEET 2 AA5 2 LEU A 273 ALA A 274 -1 O ALA A 274 N LYS A 245 SHEET 1 AA6 5 GLU A 326 PHE A 330 0 SHEET 2 AA6 5 SER A 378 LEU A 383 1 O ILE A 380 N GLU A 326 SHEET 3 AA6 5 GLN A 428 VAL A 432 -1 O LEU A 431 N TYR A 379 SHEET 4 AA6 5 PHE A 400 ALA A 404 -1 N LYS A 401 O ALA A 430 SHEET 5 AA6 5 PHE A 415 THR A 416 -1 O THR A 416 N PHE A 400 SHEET 1 AA7 3 ALA A 371 THR A 372 0 SHEET 2 AA7 3 MET A 454 ALA A 458 1 O ALA A 456 N ALA A 371 SHEET 3 AA7 3 TRP A 439 HIS A 442 -1 N TRP A 439 O ILE A 457 SHEET 1 AA8 2 HIS A 391 HIS A 394 0 SHEET 2 AA8 2 THR A 418 LEU A 421 -1 O TYR A 419 N ILE A 393 LINK NE2 HIS A 96 CU3 C2O A 501 1555 1555 2.22 LINK NE2 HIS A 96 CU CU A 502 1555 1555 2.27 LINK ND1 HIS A 98 CU2 C2O A 501 1555 1555 2.35 LINK NE2 HIS A 138 CU2 C2O A 501 1555 1555 2.69 LINK NE2 HIS A 140 CU3 C2O A 501 1555 1555 2.59 LINK ND1 HIS A 391 CU CU A 503 1555 1555 2.43 LINK NE2 HIS A 394 CU CU A 502 1555 1555 2.30 LINK NE2 HIS A 396 CU3 C2O A 501 1555 1555 2.66 LINK SG CYS A 443 CU CU A 503 1555 1555 2.23 LINK NE2 HIS A 444 CU2 C2O A 501 1555 1555 2.57 LINK ND1 HIS A 448 CU CU A 503 1555 1555 2.50 CISPEP 1 ALA A 68 PRO A 69 0 10.34 SITE 1 AC1 9 HIS A 96 HIS A 98 HIS A 138 HIS A 140 SITE 2 AC1 9 HIS A 394 HIS A 396 HIS A 442 HIS A 444 SITE 3 AC1 9 CU A 502 SITE 1 AC2 6 HIS A 96 HIS A 98 GLY A 99 HIS A 394 SITE 2 AC2 6 HIS A 396 C2O A 501 SITE 1 AC3 4 HIS A 391 CYS A 443 VAL A 445 HIS A 448 CRYST1 170.350 170.350 131.000 90.00 90.00 120.00 P 62 2 2 12 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 0.005870 0.003389 0.000000 0.00000 SCALE2 0.000000 0.006778 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007634 0.00000