HEADER REDUCTASE 18-MAR-03 1OE3 TITLE ATOMIC RESOLUTION STRUCTURE OF 'HALF APO' NIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NITRITE REDUCTASE, NIR; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: LOSS OF T1 AND T2 CU SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACHROMOBACTER XYLOSOXIDANS; SOURCE 3 ORGANISM_TAXID: 85698; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 OTHER_DETAILS: SYNTHETIC GENE KEYWDS REDUCTASE, NITRITE REDUCTASE, COPPER PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.J.ELLIS,F.E.DODD,G.SAWERS,R.R.EADY,S.S.HASNAIN REVDAT 6 11-MAR-20 1OE3 1 SEQRES REVDAT 5 22-MAY-19 1OE3 1 REMARK LINK REVDAT 4 24-FEB-09 1OE3 1 VERSN REVDAT 3 16-NOV-04 1OE3 1 HET REVDAT 2 29-JUL-04 1OE3 1 SOURCE DBREF REVDAT 1 21-JUL-04 1OE3 0 JRNL AUTH M.J.ELLIS,F.E.DODD,G.SAWERS,R.R.EADY,S.S.HASNAIN JRNL TITL ATOMIC RESOLUTION STRUCTURES OF NATIVE COPPER NITRITE JRNL TITL 2 REDUCTASE FROM ALCALIGENES XYLOSOXIDANS AND THE ACTIVE SITE JRNL TITL 3 MUTANT ASP92GLU JRNL REF J.MOL.BIOL. V. 328 429 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12691751 JRNL DOI 10.1016/S0022-2836(03)00308-5 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.114 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.116 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.148 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 2.700 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3186 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 116696 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.098 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.105 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.131 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 2.700 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2585 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 94671 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2574 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 553 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3083.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2457.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 6 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 28176 REMARK 3 NUMBER OF RESTRAINTS : 30366 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.036 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.087 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.089 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.035 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY ? REMARK 4 REMARK 4 1OE3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1290012092. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 110729 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.28300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG MME 550, 0.1M MES PH 6.5, 10MM REMARK 280 ZNSO4, PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 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 0.00000 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 49.83950 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 49.83950 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 49.83950 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 -39.62150 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 68.62645 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 39.62150 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 68.62645 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2087 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2126 LIES ON A SPECIAL POSITION. REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ARG A 336 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 5 CE NZ REMARK 480 LYS A 10 CD CE NZ REMARK 480 LYS A 27 CD CE NZ REMARK 480 LYS A 31 CE NZ REMARK 480 ASP A 48 OD1 OD2 REMARK 480 LYS A 186 CE NZ REMARK 480 LYS A 217 CG CD CE NZ REMARK 480 LYS A 230 CG CD CE NZ REMARK 480 LYS A 319 CD CE NZ REMARK 480 LYS A 329 CE NZ 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 ARG A 336 O HOH A 2538 0.81 REMARK 500 NZ LYS A 10 O HOH A 2049 0.89 REMARK 500 C2 PG4 A 999 O HOH A 2548 1.10 REMARK 500 C5 PG4 A 998 O HOH A 2541 1.28 REMARK 500 C ARG A 336 O HOH A 2538 1.31 REMARK 500 C3 PG4 A 999 O HOH A 2547 1.32 REMARK 500 C4 PG4 A 998 O HOH A 2541 1.38 REMARK 500 OD1 ASP A 323 O HOH A 2512 1.58 REMARK 500 O2 PG4 A 999 O HOH A 2548 1.59 REMARK 500 O HOH A 2163 O HOH A 2164 1.68 REMARK 500 O2 PG4 A 999 O HOH A 2547 1.72 REMARK 500 O1 PG4 A 999 O HOH A 2548 1.74 REMARK 500 O HOH A 2439 O HOH A 2480 1.95 REMARK 500 O HOH A 2060 O HOH A 2227 1.96 REMARK 500 O HOH A 2209 O HOH A 2303 1.96 REMARK 500 C4 PG4 A 999 O HOH A 2547 1.96 REMARK 500 CA ARG A 336 O HOH A 2538 2.00 REMARK 500 O1 PG4 A 999 O HOH A 2551 2.01 REMARK 500 C2 PG4 A 999 O HOH A 2547 2.10 REMARK 500 O HOH A 2099 O HOH A 2103 2.15 REMARK 500 O HOH A 2506 O HOH A 2519 2.16 REMARK 500 OE1 GLU A 195 O HOH A 2389 2.18 REMARK 500 OD2 ASP A 323 O HOH A 2511 2.19 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 2447 O HOH A 2458 3565 1.86 REMARK 500 O HOH A 2440 O HOH A 2440 2665 2.10 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 ARG A 244 NE ARG A 244 CZ -0.099 REMARK 500 ARG A 244 CZ ARG A 244 NH1 0.085 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 MET A 62 CG - SD - CE ANGL. DEV. = -10.0 DEGREES REMARK 500 ARG A 153 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 153 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 168 NE - CZ - NH1 ANGL. DEV. = -7.4 DEGREES REMARK 500 ARG A 168 NE - CZ - NH2 ANGL. DEV. = 6.7 DEGREES REMARK 500 TYR A 197 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 TYR A 197 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 MET A 204 CG - SD - CE ANGL. DEV. = -11.1 DEGREES REMARK 500 ARG A 244 NH1 - CZ - NH2 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG A 244 NE - CZ - NH2 ANGL. DEV. = -5.7 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 GLN A 24 -96.85 -87.73 REMARK 500 ALA A 131 65.52 -155.55 REMARK 500 MET A 135 39.79 -146.85 REMARK 500 LEU A 221 49.94 -103.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 300 ASN A 301 145.62 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 A2016 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A2055 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH A2087 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A2089 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A2098 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A2107 DISTANCE = 6.86 ANGSTROMS REMARK 525 HOH A2146 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH A2151 DISTANCE = 7.37 ANGSTROMS REMARK 525 HOH A2200 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A2206 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A2220 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A2270 DISTANCE = 6.14 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 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 144 SD REMARK 620 2 HIS A 139 ND1 120.2 REMARK 620 3 CYS A 130 SG 110.3 113.7 REMARK 620 4 HIS A 89 ND1 91.1 95.7 124.2 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 HOH A2253 O REMARK 620 2 HIS A 300 NE2 109.6 REMARK 620 3 HIS A 129 NE2 112.7 110.4 REMARK 620 4 HIS A 94 NE2 109.9 105.8 108.2 REMARK 620 N 1 2 3 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. 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 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 998 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BQ5 RELATED DB: PDB REMARK 900 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS GIFU 1051 REMARK 900 RELATED ID: 1GS6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF M144A MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE REMARK 900 RELATED ID: 1GS7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF H254F MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE REMARK 900 RELATED ID: 1GS8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF M144A MUTANT OF ALCALIGENES XYLOSOXIDANS REMARK 900 NITRITE REDUCTASE REMARK 900 RELATED ID: 1HAU RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND REMARK 900 IN COPPER FREE FORM AT 1.9E RESOLUTION REMARK 900 RELATED ID: 1HAW RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND REMARK 900 IN COPPER FREE FORM AT 1.9E RESOLUTION REMARK 900 RELATED ID: 1NDT RELATED DB: PDB REMARK 900 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS REMARK 900 RELATED ID: 1OE1 RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF THE WILDTYPE NATIVE NITRITE REMARK 900 REDUCTASE FROM ALCALIGENES XYLOSOXIDANS REMARK 900 RELATED ID: 1OE2 RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF D92E MUTANT OF ALCALIGENES REMARK 900 XYLOSOXIDANS NITRITE REDUCTASE DBREF 1OE3 A 1 336 UNP O68601 O68601 25 360 SEQRES 1 A 336 PCA ASP ALA ASP LYS LEU PRO HIS THR LYS VAL THR LEU SEQRES 2 A 336 VAL ALA PRO PRO GLN VAL HIS PRO HIS GLU GLN ALA THR SEQRES 3 A 336 LYS SER GLY PRO LYS VAL VAL GLU PHE THR MET THR ILE SEQRES 4 A 336 GLU GLU LYS LYS MET VAL ILE ASP ASP LYS GLY THR THR SEQRES 5 A 336 LEU GLN ALA MET THR PHE ASN GLY SER MET PRO GLY PRO SEQRES 6 A 336 THR LEU VAL VAL HIS GLU GLY ASP TYR VAL GLN LEU THR SEQRES 7 A 336 LEU VAL ASN PRO ALA THR ASN ALA MET PRO HIS ASN VAL SEQRES 8 A 336 ASP PHE HIS GLY ALA THR GLY ALA LEU GLY GLY ALA LYS SEQRES 9 A 336 LEU THR ASN VAL ASN PRO GLY GLU GLN ALA THR LEU ARG SEQRES 10 A 336 PHE LYS ALA ASP ARG SER GLY THR PHE VAL TYR HIS CYS SEQRES 11 A 336 ALA PRO GLU GLY MET VAL PRO TRP HIS VAL VAL SER GLY SEQRES 12 A 336 MET SER GLY THR LEU MET VAL LEU PRO ARG ASP GLY LEU SEQRES 13 A 336 LYS ASP PRO GLN GLY LYS PRO LEU HIS TYR ASP ARG ALA SEQRES 14 A 336 TYR THR ILE GLY GLU PHE ASP LEU TYR ILE PRO LYS GLY SEQRES 15 A 336 PRO ASP GLY LYS TYR LYS ASP TYR ALA THR LEU ALA GLU SEQRES 16 A 336 SER TYR GLY ASP THR VAL GLN VAL MET ARG THR LEU THR SEQRES 17 A 336 PRO SER HIS ILE VAL PHE ASN GLY LYS VAL GLY ALA LEU SEQRES 18 A 336 THR GLY ALA ASN ALA LEU THR ALA LYS VAL GLY GLU THR SEQRES 19 A 336 VAL LEU LEU ILE HIS SER GLN ALA ASN ARG ASP THR ARG SEQRES 20 A 336 PRO HIS LEU ILE GLY GLY HIS GLY ASP TRP VAL TRP GLU SEQRES 21 A 336 THR GLY LYS PHE ALA ASN PRO PRO GLN ARG ASP LEU GLU SEQRES 22 A 336 THR TRP PHE ILE ARG GLY GLY SER ALA GLY ALA ALA LEU SEQRES 23 A 336 TYR THR PHE LYS GLN PRO GLY VAL TYR ALA TYR LEU ASN SEQRES 24 A 336 HIS ASN LEU ILE GLU ALA PHE GLU LEU GLY ALA ALA GLY SEQRES 25 A 336 HIS ILE LYS VAL GLU GLY LYS TRP ASN ASP ASP LEU MET SEQRES 26 A 336 LYS GLN ILE LYS ALA PRO ALA PRO ILE PRO ARG MODRES 1OE3 PCA A 1 GLU PYROGLUTAMIC ACID HET PCA A 1 8 HET CU A 501 1 HET CU A 502 1 HET PG4 A 998 10 HET PG4 A 999 13 HETNAM PCA PYROGLUTAMIC ACID HETNAM CU COPPER (II) ION HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 1 PCA C5 H7 N O3 FORMUL 2 CU 2(CU 2+) FORMUL 4 PG4 2(C8 H18 O5) FORMUL 6 HOH *553(H2 O) HELIX 1 1 GLY A 98 THR A 106 5 9 HELIX 2 2 MET A 135 SER A 142 1 8 HELIX 3 3 THR A 192 THR A 206 1 15 HELIX 4 4 THR A 222 ALA A 226 5 5 HELIX 5 5 ASN A 301 GLU A 307 1 7 SHEET 1 AA 4 HIS A 8 THR A 9 0 SHEET 2 AA 4 VAL A 32 VAL A 45 1 O VAL A 32 N THR A 9 SHEET 3 AA 4 TYR A 74 ASN A 81 1 O TYR A 74 N VAL A 33 SHEET 4 AA 4 GLU A 112 LYS A 119 -1 O GLU A 112 N ASN A 81 SHEET 1 AB 3 HIS A 8 THR A 9 0 SHEET 2 AB 3 VAL A 32 VAL A 45 1 O VAL A 32 N THR A 9 SHEET 3 AB 3 THR A 52 PHE A 58 -1 O LEU A 53 N MET A 44 SHEET 1 AC 4 LEU A 67 HIS A 70 0 SHEET 2 AC 4 SER A 145 LEU A 151 1 O THR A 147 N LEU A 67 SHEET 3 AC 4 GLY A 124 HIS A 129 -1 O GLY A 124 N VAL A 150 SHEET 4 AC 4 ASP A 92 PHE A 93 -1 O ASP A 92 N HIS A 129 SHEET 1 AD 6 HIS A 211 PHE A 214 0 SHEET 2 AD 6 ARG A 168 LEU A 177 -1 O PHE A 175 N VAL A 213 SHEET 3 AD 6 THR A 234 GLN A 241 1 O LEU A 236 N TYR A 170 SHEET 4 AD 6 SER A 281 THR A 288 -1 O SER A 281 N GLN A 241 SHEET 5 AD 6 GLY A 255 TRP A 259 -1 N ASP A 256 O LEU A 286 SHEET 6 AD 6 GLN A 269 LEU A 272 -1 O GLN A 269 N VAL A 258 SHEET 1 AE 4 LEU A 227 LYS A 230 0 SHEET 2 AE 4 ALA A 311 GLU A 317 1 O HIS A 313 N LEU A 227 SHEET 3 AE 4 GLY A 293 ASN A 299 -1 O GLY A 293 N VAL A 316 SHEET 4 AE 4 PRO A 248 LEU A 250 -1 O HIS A 249 N LEU A 298 LINK C PCA A 1 N ASP A 2 1555 1555 1.34 LINK O ALA A 83 O4 PG4 A 998 5564 1555 1.97 LINK CU CU A 501 SD MET A 144 1555 1555 2.51 LINK CU CU A 501 ND1 HIS A 139 1555 1555 2.10 LINK CU CU A 501 SG CYS A 130 1555 1555 2.22 LINK CU CU A 501 ND1 HIS A 89 1555 1555 1.99 LINK CU CU A 502 O HOH A2253 1555 1555 1.89 LINK CU CU A 502 NE2 HIS A 300 1555 3565 1.93 LINK CU CU A 502 NE2 HIS A 129 1555 1555 1.99 LINK CU CU A 502 NE2 HIS A 94 1555 1555 1.93 CISPEP 1 PRO A 16 PRO A 17 0 5.71 CISPEP 2 MET A 62 PRO A 63 0 -9.40 SITE 1 AC1 5 ASP A 92 HIS A 94 HIS A 129 HIS A 300 SITE 2 AC1 5 HOH A2253 SITE 1 AC2 4 HIS A 89 CYS A 130 HIS A 139 MET A 144 SITE 1 AC3 12 GLU A 133 VAL A 294 ALA A 296 PHE A 306 SITE 2 AC3 12 HIS A 313 HOH A2308 HOH A2484 HOH A2547 SITE 3 AC3 12 HOH A2548 HOH A2550 HOH A2551 HOH A2552 SITE 1 AC4 6 ALA A 83 THR A 84 LYS A 162 HOH A2541 SITE 2 AC4 6 HOH A2543 HOH A2545 CRYST1 79.243 79.243 99.679 90.00 90.00 120.00 P 63 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 0.012619 0.007286 0.000000 0.00000 SCALE2 0.000000 0.014572 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010032 0.00000 MASTER 454 0 5 5 21 0 8 6 0 0 0 26 END