HEADER OXIDOREDUCTASE 31-JAN-20 6VOW TITLE CRYSTAL STRUCTURE OF MULTI-COPPER OXIDASE FROM PSEUDOMONAS TITLE 2 THERMOTOLERANS CAVEAT 6VOW RESIDUES VAL A 422 AND ALA A 423 THAT ARE NEXT TO EACH OTHER CAVEAT 2 6VOW IN THE SAMPLE SEQUENCE ARE NOT PROPERLY LINKED: DISTANCE CAVEAT 3 6VOW BETWEEN C AND N IS 1.91 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTICOPPER OXIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS THERMOTOLERANS; SOURCE 3 ORGANISM_TAXID: 157784; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, LACCASE, COPPER OXIDASE, ACOUSTIC DROPLET EJECTION, KEYWDS 2 LIGNIN EXPDTA X-RAY DIFFRACTION AUTHOR E.A.COLER,A.S.SOARES,R.E.COLLINS REVDAT 2 11-OCT-23 6VOW 1 REMARK REVDAT 1 03-FEB-21 6VOW 0 JRNL AUTH E.A.COLER,A.S.SOARES,R.E.COLLINS JRNL TITL CRYSTAL STRUCTURE OF MULTI-COPPER OXIDASE FROM PSEUDOMONAS JRNL TITL 2 THERMOTOLERANS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.92 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 3 NUMBER OF REFLECTIONS : 29668 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1590 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) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1577 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.3300 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3227 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 136 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.79000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : -0.80000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.86000 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): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.133 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.056 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3389 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3189 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4612 ; 2.408 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7321 ; 1.154 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 416 ; 8.031 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;35.814 ;22.595 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 522 ;17.073 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;20.698 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 494 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3841 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 803 ; 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): 1658 ; 8.246 ; 4.959 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1657 ; 8.235 ; 5.184 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2076 ; 9.415 ; 7.435 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2077 ; 9.416 ;29.751 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1730 ;10.401 ; 5.496 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1729 ;10.403 ; 5.497 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2536 ;11.268 ; 8.053 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3879 ;10.690 ;41.230 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3848 ;10.654 ;41.136 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6575 ; 4.848 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 43 ;34.087 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6564 ;20.341 ; 5.000 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 6VOW 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_1000246789. 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 : NULL 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 : 31326 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 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 (%) : 90.2 REMARK 200 DATA REDUNDANCY : 19.36 REMARK 200 R MERGE (I) : 0.42000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.50200 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: 4F7K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 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: 0.10 M AMMONIUM ACETATE 10 %(W/V) PEG 3350 REMARK 280 SOLUTION WAS EQUILIBRATED AGAINST A RESERVOIR OF 60% PEG 3350., REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 67.55500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.42000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.55500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.42000 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 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 MET A -32 REMARK 465 ALA A -31 REMARK 465 PHE A -30 REMARK 465 THR A -29 REMARK 465 ARG A -28 REMARK 465 ARG A -27 REMARK 465 GLN A -26 REMARK 465 VAL A -25 REMARK 465 LEU A -24 REMARK 465 GLY A -23 REMARK 465 GLY A -22 REMARK 465 LEU A -21 REMARK 465 VAL A -20 REMARK 465 GLY A -19 REMARK 465 LEU A -18 REMARK 465 GLY A -17 REMARK 465 VAL A -16 REMARK 465 VAL A -15 REMARK 465 GLY A -14 REMARK 465 LEU A -13 REMARK 465 GLY A -12 REMARK 465 ALA A -11 REMARK 465 GLY A -10 REMARK 465 GLY A -9 REMARK 465 VAL A -8 REMARK 465 ARG A -7 REMARK 465 TYR A -6 REMARK 465 TRP A -5 REMARK 465 LEU A -4 REMARK 465 GLY A -3 REMARK 465 ARG A -2 REMARK 465 PRO A -1 REMARK 465 GLU A 0 REMARK 465 TRP A 298 REMARK 465 ALA A 299 REMARK 465 ALA A 300 REMARK 465 THR A 301 REMARK 465 LEU A 302 REMARK 465 VAL A 303 REMARK 465 ASP A 304 REMARK 465 ASN A 305 REMARK 465 LEU A 306 REMARK 465 ALA A 307 REMARK 465 GLN A 308 REMARK 465 GLY A 309 REMARK 465 GLY A 310 REMARK 465 SER A 311 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 GLU A 267 CG CD OE1 OE2 REMARK 470 TYR A 312 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR A 314 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 320 CG CD OE1 NE2 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 647 O HOH A 710 2.11 REMARK 500 OG SER A 369 OE2 GLU A 388 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 618 O HOH A 700 2656 2.05 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 SER A 78 CB SER A 78 OG 0.114 REMARK 500 GLU A 297 CG GLU A 297 CD 0.100 REMARK 500 TRP A 322 CB TRP A 322 CG 0.145 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 ARG A 39 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 39 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 173 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 240 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 240 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 246 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 323 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 CYS A 329 CA - CB - SG ANGL. DEV. = 6.9 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 PRO A 20 139.01 -39.69 REMARK 500 ASP A 144 -168.32 -77.95 REMARK 500 ARG A 160 -124.48 -104.15 REMARK 500 THR A 196 -27.68 -143.25 REMARK 500 LYS A 313 -153.53 -156.17 REMARK 500 TYR A 314 93.53 -68.49 REMARK 500 ARG A 332 78.69 -117.05 REMARK 500 LEU A 350 51.19 -90.78 REMARK 500 LEU A 367 -63.50 -95.38 REMARK 500 ARG A 371 -60.62 -100.12 REMARK 500 ASN A 387 27.56 48.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 734 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 735 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A 736 DISTANCE = 7.09 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 502 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 61 NE2 REMARK 620 2 HIS A 358 NE2 174.1 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 63 ND1 REMARK 620 2 C2O A 501 O1 113.6 REMARK 620 3 HIS A 103 NE2 137.8 99.0 REMARK 620 4 HIS A 407 NE2 104.8 75.0 109.1 REMARK 620 N 1 2 3 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 105 NE2 REMARK 620 2 C2O A 501 O1 116.9 REMARK 620 3 HIS A 360 NE2 103.7 112.9 REMARK 620 4 HIS A 405 NE2 114.7 93.1 116.2 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 355 ND1 REMARK 620 2 CYS A 406 SG 135.1 REMARK 620 3 HIS A 411 ND1 99.8 125.0 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: 6VOX RELATED DB: PDB REMARK 900 COPPER OXIDASE SOLVED DURING SAME PROJECT DBREF 6VOW A -32 423 PDB 6VOW 6VOW -32 423 SEQRES 1 A 456 MET ALA PHE THR ARG ARG GLN VAL LEU GLY GLY LEU VAL SEQRES 2 A 456 GLY LEU GLY VAL VAL GLY LEU GLY ALA GLY GLY VAL ARG SEQRES 3 A 456 TYR TRP LEU GLY ARG PRO GLU SER ALA VAL THR HIS ASP SEQRES 4 A 456 TYR GLU LEU ILE ALA ALA PRO VAL ASP MET GLU LEU VAL SEQRES 5 A 456 PRO GLY HIS VAL THR PRO ALA TRP GLY TYR GLY GLY GLN SEQRES 6 A 456 ALA PRO GLY VAL GLU LEU ARG CYS ARG GLN GLY ASP TRP SEQRES 7 A 456 LEU ARG VAL ARG PHE ILE ASN LYS LEU ASP GLU PRO THR SEQRES 8 A 456 THR ILE HIS TRP HIS GLY ILE ARG LEU PRO LEU GLU MET SEQRES 9 A 456 ASP GLY VAL PRO TYR VAL SER GLN LEU PRO VAL GLN PRO SEQRES 10 A 456 GLY GLU TYR PHE ASP TYR VAL PHE LYS THR GLU ASP ALA SEQRES 11 A 456 GLY ASN PHE TRP TYR HIS PRO HIS GLU SER SER ALA SER SEQRES 12 A 456 GLN LEU GLY ARG GLY LEU VAL GLY PRO LEU VAL VAL GLU SEQRES 13 A 456 GLU ARG GLU PRO SER GLY PHE ARG HIS GLU LEU SER LEU SEQRES 14 A 456 SER LEU LYS THR TRP HIS VAL ASP GLU GLN GLY ALA PHE SEQRES 15 A 456 THR PRO PHE MET VAL PRO ARG GLU ALA ALA ARG GLU GLY SEQRES 16 A 456 THR ARG GLY ARG LEU THR THR VAL ASN ALA ARG PRO ASN SEQRES 17 A 456 PRO THR LEU GLU LEU PRO ALA GLY GLN VAL VAL ARG LEU SEQRES 18 A 456 ARG LEU PHE ASN LEU ASP ASN THR VAL THR TYR ARG LEU SEQRES 19 A 456 ASN LEU PRO GLY ALA GLU ALA ARG LEU TYR ALA LEU ASP SEQRES 20 A 456 GLY HIS PRO ILE GLU PRO ARG PRO LEU GLY LYS GLU TYR SEQRES 21 A 456 TRP LEU GLY PRO GLY MET ARG ILE ASP LEU ALA VAL ARG SEQRES 22 A 456 VAL PRO GLU ALA GLY ARG GLU LEU PRO LEU ARG ASN GLY SEQRES 23 A 456 PRO LEU ARG LEU ALA THR LEU LYS SER VAL ALA SER VAL SEQRES 24 A 456 GLU ALA PRO GLY ASP TRP PRO ALA PRO LEU PRO ALA ASN SEQRES 25 A 456 PRO VAL ALA GLU PRO ASP LEU SER ILE ALA GLU THR LEU SEQRES 26 A 456 SER PHE ARG PHE GLU TRP ALA ALA THR LEU VAL ASP ASN SEQRES 27 A 456 LEU ALA GLN GLY GLY SER TYR LYS TYR TRP GLN ILE ASN SEQRES 28 A 456 GLY GLN ALA TRP ASP ILE ASN ASP ILE SER CYS ALA GLU SEQRES 29 A 456 ARG PRO ILE ALA THR LEU LYS LYS GLY GLY HIS TYR ILE SEQRES 30 A 456 PHE GLU LEU ARG ASN LEU ALA GLN TYR GLN HIS PRO ILE SEQRES 31 A 456 HIS LEU HIS GLY MET VAL PHE LYS VAL LEU SER SER ASP SEQRES 32 A 456 ARG ARG GLU ILE ILE PRO TYR PHE THR ASP THR TYR LEU SEQRES 33 A 456 LEU GLY LYS ASN GLU THR ALA ARG VAL ALA LEU VAL ALA SEQRES 34 A 456 ASP ASN PRO GLY VAL TRP MET PHE HIS CYS HIS VAL ILE SEQRES 35 A 456 ASP HIS MET GLU THR GLY LEU MET ALA ALA ILE GLU VAL SEQRES 36 A 456 ALA 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+) FORMUL 5 HOH *136(H2 O) HELIX 1 AA1 PRO A 68 ASP A 72 5 5 HELIX 2 AA2 SER A 107 ARG A 114 1 8 HELIX 3 AA3 VAL A 154 ALA A 159 1 6 HELIX 4 AA4 VAL A 408 THR A 414 1 7 SHEET 1 AA1 4 THR A 24 TYR A 29 0 SHEET 2 AA1 4 THR A 4 MET A 16 -1 N VAL A 14 O ALA A 26 SHEET 3 AA1 4 TRP A 45 ASN A 52 1 O ARG A 47 N HIS A 5 SHEET 4 AA1 4 TYR A 87 LYS A 93 -1 O PHE A 88 N PHE A 50 SHEET 1 AA2 4 LEU A 38 ARG A 41 0 SHEET 2 AA2 4 GLY A 118 GLU A 123 1 O VAL A 121 N LEU A 38 SHEET 3 AA2 4 GLY A 98 HIS A 103 -1 N PHE A 100 O LEU A 120 SHEET 4 AA2 4 HIS A 61 HIS A 63 -1 N HIS A 61 O HIS A 103 SHEET 1 AA3 6 LEU A 167 VAL A 170 0 SHEET 2 AA3 6 HIS A 132 TRP A 141 -1 N TRP A 141 O LEU A 167 SHEET 3 AA3 6 VAL A 185 ASN A 192 1 O ARG A 189 N LEU A 134 SHEET 4 AA3 6 ARG A 234 ARG A 240 -1 O LEU A 237 N LEU A 188 SHEET 5 AA3 6 GLU A 207 LEU A 213 -1 N ARG A 209 O ALA A 238 SHEET 6 AA3 6 HIS A 216 PRO A 222 -1 O ARG A 221 N LEU A 210 SHEET 1 AA4 5 THR A 177 PRO A 181 0 SHEET 2 AA4 5 LEU A 255 VAL A 263 1 O VAL A 263 N LEU A 180 SHEET 3 AA4 5 GLU A 247 ASN A 252 -1 N LEU A 250 O ALA A 258 SHEET 4 AA4 5 TYR A 199 ASN A 202 -1 N ASN A 202 O ARG A 251 SHEET 5 AA4 5 TYR A 227 LEU A 229 -1 O LEU A 229 N TYR A 199 SHEET 1 AA5 5 GLU A 290 PHE A 296 0 SHEET 2 AA5 5 HIS A 342 ASN A 349 1 O ILE A 344 N GLU A 290 SHEET 3 AA5 5 THR A 389 VAL A 395 -1 O ALA A 390 N LEU A 347 SHEET 4 AA5 5 PHE A 364 SER A 369 -1 N LYS A 365 O ALA A 393 SHEET 5 AA5 5 TYR A 377 THR A 379 -1 O TYR A 377 N VAL A 366 SHEET 1 AA6 5 ALA A 335 LYS A 338 0 SHEET 2 AA6 5 MET A 417 ALA A 423 1 O GLU A 421 N LEU A 337 SHEET 3 AA6 5 GLY A 400 CYS A 406 -1 N GLY A 400 O VAL A 422 SHEET 4 AA6 5 HIS A 355 LEU A 359 -1 N HIS A 358 O HIS A 405 SHEET 5 AA6 5 THR A 381 LEU A 384 -1 O LEU A 384 N HIS A 355 LINK NE2 HIS A 61 CU CU A 502 1555 1555 2.00 LINK ND1 HIS A 63 CU2 C2O A 501 1555 1555 2.08 LINK NE2 HIS A 103 CU2 C2O A 501 1555 1555 2.01 LINK NE2 HIS A 105 CU3 C2O A 501 1555 1555 2.20 LINK ND1 HIS A 355 CU CU A 503 1555 1555 2.02 LINK NE2 HIS A 358 CU CU A 502 1555 1555 1.97 LINK NE2 HIS A 360 CU3 C2O A 501 1555 1555 2.19 LINK NE2 HIS A 405 CU3 C2O A 501 1555 1555 2.24 LINK SG CYS A 406 CU CU A 503 1555 1555 2.22 LINK NE2 HIS A 407 CU2 C2O A 501 1555 1555 2.06 LINK ND1 HIS A 411 CU CU A 503 1555 1555 2.07 CISPEP 1 ALA A 33 PRO A 34 0 -1.31 CISPEP 2 PHE A 296 GLU A 297 0 -20.39 SITE 1 AC1 10 HIS A 61 HIS A 63 TRP A 101 HIS A 103 SITE 2 AC1 10 HIS A 105 HIS A 358 HIS A 360 HIS A 405 SITE 3 AC1 10 HIS A 407 CU A 502 SITE 1 AC2 4 HIS A 61 HIS A 358 HIS A 360 C2O A 501 SITE 1 AC3 4 HIS A 355 CYS A 406 HIS A 411 LEU A 416 CRYST1 135.110 68.840 49.520 90.00 93.05 90.00 C 1 2 1 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 0.007401 0.000000 0.000395 0.00000 SCALE2 0.000000 0.014526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020223 0.00000