HEADER OXIDOREDUCTASE 18-SEP-98 2NAP TITLE DISSIMILATORY NITRATE REDUCTASE (NAP) FROM DESULFOVIBRIO DESULFURICANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (PERIPLASMIC NITRATE REDUCTASE); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO DESULFURICANS; SOURCE 3 ORGANISM_TAXID: 876; SOURCE 4 COLLECTION: ATCC 27774; SOURCE 5 CELLULAR_LOCATION: PERIPLASM KEYWDS NITROGENOUS ACCEPTOR, DISSIMILATORY NITRATE REDUCTASE, KEYWDS 2 MULTIWAVELENGTH ANOMALOUS DIFFRACTION, MOLYBDOPTERIN COFACTOR, [4FE- KEYWDS 3 4S] CLUSTER, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.DIAS,M.THAN,A.HUMM,R.HUBER,G.BOURENKOV,H.BARTUNIK,S.BURSAKOV, AUTHOR 2 J.CALVETE,J.CALDEIRA,C.CARNEIRO,J.MOURA,I.MOURA,M.J.ROMAO REVDAT 5 27-DEC-23 2NAP 1 REMARK SEQADV LINK REVDAT 4 06-FEB-19 2NAP 1 REMARK ATOM REVDAT 3 24-FEB-09 2NAP 1 VERSN REVDAT 2 01-APR-03 2NAP 1 JRNL REVDAT 1 19-SEP-99 2NAP 0 JRNL AUTH J.M.DIAS,M.E.THAN,A.HUMM,R.HUBER,G.P.BOURENKOV,H.D.BARTUNIK, JRNL AUTH 2 S.BURSAKOV,J.CALVETE,J.CALDEIRA,C.CARNEIRO,J.J.MOURA, JRNL AUTH 3 I.MOURA,M.J.ROMAO JRNL TITL CRYSTAL STRUCTURE OF THE FIRST DISSIMILATORY NITRATE JRNL TITL 2 REDUCTASE AT 1.9 A SOLVED BY MAD METHODS. JRNL REF STRUCTURE FOLD.DES. V. 7 65 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10368307 JRNL DOI 10.1016/S0969-2126(99)80010-0 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 66798 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 SET) : 0.218 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4225 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5591 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 115 REMARK 3 SOLVENT ATOMS : 595 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 2.010 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000007117. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MPG/DESY, HAMBURG REMARK 200 BEAMLINE : BW6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.7219,1.7389,1.1000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69767 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP, CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -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 44.97000 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 89.94000 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 89.94000 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 44.97000 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 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 1 REMARK 465 ASP A 2 REMARK 465 ASN A 3 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 ARG A 4 CB CG CD NE CZ NH1 NH2 REMARK 470 GLU A 6 CG CD OE1 OE2 REMARK 470 LYS A 7 CG CD CE NZ REMARK 470 LYS A 259 CD CE NZ REMARK 470 GLU A 287 CG CD OE1 OE2 REMARK 470 LYS A 380 CD CE NZ REMARK 470 GLU A 386 CD OE1 OE2 REMARK 470 GLU A 541 CD OE1 OE2 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 27 CE NZ REMARK 480 LYS A 75 CD CE NZ REMARK 480 GLN A 193 CG REMARK 480 GLU A 257 OE1 OE2 REMARK 480 GLN A 510 CG CD OE1 NE2 REMARK 480 ARG A 544 NH1 NH2 REMARK 480 GLU A 608 CG REMARK 480 LYS A 636 NZ REMARK 480 GLU A 647 OE1 OE2 REMARK 480 GLU A 648 CB CG CD OE1 OE2 REMARK 480 ARG A 652 CG CD NE CZ NH1 NH2 REMARK 480 THR A 653 CB OG1 CG2 REMARK 480 LYS A 722 NZ 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 MET A 308 C GLY A 309 N 0.197 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 67 CA - CB - CG ANGL. DEV. = 15.0 DEGREES REMARK 500 CYS A 307 O - C - N ANGL. DEV. = -15.0 DEGREES REMARK 500 MET A 308 O - C - N ANGL. DEV. = -26.2 DEGREES REMARK 500 ARG A 515 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 PRO A 610 C - N - CA ANGL. DEV. = 9.2 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 TYR A 15 -126.71 -96.24 REMARK 500 ASP A 28 92.88 35.43 REMARK 500 LEU A 52 35.61 -97.64 REMARK 500 ASN A 102 6.86 -62.10 REMARK 500 CYS A 140 -68.12 -137.86 REMARK 500 GLU A 156 148.99 74.48 REMARK 500 ASN A 176 70.66 -101.18 REMARK 500 ASP A 204 135.89 -174.20 REMARK 500 ASP A 255 -179.23 -64.08 REMARK 500 SER A 261 -154.79 -144.66 REMARK 500 CYS A 307 -135.87 -139.17 REMARK 500 ALA A 358 46.04 -92.50 REMARK 500 GLU A 386 133.40 -34.82 REMARK 500 TRP A 464 -116.31 33.30 REMARK 500 VAL A 512 50.20 -111.76 REMARK 500 ASP A 534 101.27 -8.59 REMARK 500 SER A 547 60.64 -101.54 REMARK 500 TYR A 584 -4.63 -56.70 REMARK 500 LYS A 599 -128.33 -114.63 REMARK 500 HIS A 623 -114.43 39.73 REMARK 500 ASP A 668 167.59 176.12 REMARK 500 SER A 677 -169.82 -161.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 CYS A 307 12.40 REMARK 500 MET A 308 32.74 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 A1415 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A1493 DISTANCE = 5.83 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 SF4 A 800 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 13 SG REMARK 620 2 SF4 A 800 S1 106.8 REMARK 620 3 SF4 A 800 S2 115.5 106.9 REMARK 620 4 SF4 A 800 S3 111.5 108.5 107.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 800 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 16 SG REMARK 620 2 SF4 A 800 S1 114.2 REMARK 620 3 SF4 A 800 S2 116.1 105.8 REMARK 620 4 SF4 A 800 S4 105.6 106.9 107.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 800 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 20 SG REMARK 620 2 SF4 A 800 S1 104.0 REMARK 620 3 SF4 A 800 S3 113.8 108.8 REMARK 620 4 SF4 A 800 S4 115.7 108.5 105.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 800 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 47 SG REMARK 620 2 SF4 A 800 S2 102.5 REMARK 620 3 SF4 A 800 S3 115.1 106.3 REMARK 620 4 SF4 A 800 S4 118.3 108.0 105.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MO A 810 MO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 140 SG REMARK 620 2 MGD A 811 S12 126.6 REMARK 620 3 MGD A 811 S13 89.9 76.4 REMARK 620 4 MGD A 812 S13 146.5 83.0 114.8 REMARK 620 5 MGD A 812 S12 81.7 145.3 85.1 78.5 REMARK 620 6 HOH A 813 O 55.2 103.0 136.8 107.9 110.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: FS4 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: 4 IRON - 4 SULFUR CLUSTER REMARK 800 REMARK 800 SITE_IDENTIFIER: MGD REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: MOLYBDOPTERIN GUANINE DINUCLEOTIDE COFACTOR REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MO A 810 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MGD A 811 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MGD A 812 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 2300 DBREF 2NAP A 1 723 GB 38209021 CAA77019 33 755 SEQADV 2NAP ASN A 37 GB 38209021 ASP 69 CONFLICT SEQRES 1 A 723 ALA ASP ASN ARG PRO GLU LYS TRP VAL LYS GLY VAL CYS SEQRES 2 A 723 ARG TYR CYS GLY THR GLY CYS GLY VAL LEU VAL GLY VAL SEQRES 3 A 723 LYS ASP GLY LYS ALA VAL ALA ILE GLN GLY ASN PRO ASN SEQRES 4 A 723 ASN HIS ASN ALA GLY LEU LEU CYS LEU LYS GLY SER LEU SEQRES 5 A 723 LEU ILE PRO VAL LEU ASN SER LYS GLU ARG VAL THR GLN SEQRES 6 A 723 PRO LEU VAL ARG ARG HIS LYS GLY GLY LYS LEU GLU PRO SEQRES 7 A 723 VAL SER TRP ASP GLU ALA LEU ASP LEU MET ALA SER ARG SEQRES 8 A 723 PHE ARG SER SER ILE ASP MET TYR GLY PRO ASN SER VAL SEQRES 9 A 723 ALA TRP TYR GLY SER GLY GLN CYS LEU THR GLU GLU SER SEQRES 10 A 723 TYR VAL ALA ASN LYS ILE PHE LYS GLY GLY PHE GLY THR SEQRES 11 A 723 ASN ASN VAL ASP GLY ASN PRO ARG LEU CYS MET ALA SER SEQRES 12 A 723 ALA VAL GLY GLY TYR VAL THR SER PHE GLY LYS ASP GLU SEQRES 13 A 723 PRO MET GLY THR TYR ALA ASP ILE ASP GLN ALA THR CYS SEQRES 14 A 723 PHE PHE ILE ILE GLY SER ASN THR SER GLU ALA HIS PRO SEQRES 15 A 723 VAL LEU PHE ARG ARG ILE ALA ARG ARG LYS GLN VAL GLU SEQRES 16 A 723 PRO GLY VAL LYS ILE ILE VAL ALA ASP PRO ARG ARG THR SEQRES 17 A 723 ASN THR SER ARG ILE ALA ASP MET HIS VAL ALA PHE ARG SEQRES 18 A 723 PRO GLY THR ASP LEU ALA PHE MET HIS SER MET ALA TRP SEQRES 19 A 723 VAL ILE ILE ASN GLU GLU LEU ASP ASN PRO ARG PHE TRP SEQRES 20 A 723 GLN ARG TYR VAL ASN PHE MET ASP ALA GLU GLY LYS PRO SEQRES 21 A 723 SER ASP PHE GLU GLY TYR LYS ALA PHE LEU GLU ASN TYR SEQRES 22 A 723 ARG PRO GLU LYS VAL ALA GLU ILE CYS ARG VAL PRO VAL SEQRES 23 A 723 GLU GLN ILE TYR GLY ALA ALA ARG ALA PHE ALA GLU SER SEQRES 24 A 723 ALA ALA THR MET SER LEU TRP CYS MET GLY ILE ASN GLN SEQRES 25 A 723 ARG VAL GLN GLY VAL PHE ALA ASN ASN LEU ILE HIS ASN SEQRES 26 A 723 LEU HIS LEU ILE THR GLY GLN ILE CYS ARG PRO GLY ALA SEQRES 27 A 723 THR SER PHE SER LEU THR GLY GLN PRO ASN ALA CYS GLY SEQRES 28 A 723 GLY VAL ARG ASP GLY GLY ALA LEU SER HIS LEU LEU PRO SEQRES 29 A 723 ALA GLY ARG ALA ILE PRO ASN ALA LYS HIS ARG ALA GLU SEQRES 30 A 723 MET GLU LYS LEU TRP GLY LEU PRO GLU GLY ARG ILE ALA SEQRES 31 A 723 PRO GLU PRO GLY TYR HIS THR VAL ALA LEU PHE GLU ALA SEQRES 32 A 723 LEU GLY ARG GLY ASP VAL LYS CYS MET ILE ILE CYS GLU SEQRES 33 A 723 THR ASN PRO ALA HIS THR LEU PRO ASN LEU ASN LYS VAL SEQRES 34 A 723 HIS LYS ALA MET SER HIS PRO GLU SER PHE ILE VAL CYS SEQRES 35 A 723 ILE GLU ALA PHE PRO ASP ALA VAL THR LEU GLU TYR ALA SEQRES 36 A 723 ASP LEU VAL LEU PRO PRO ALA PHE TRP CYS GLU ARG ASP SEQRES 37 A 723 GLY VAL TYR GLY CYS GLY GLU ARG ARG TYR SER LEU THR SEQRES 38 A 723 GLU LYS ALA VAL ASP PRO PRO GLY GLN CYS ARG PRO THR SEQRES 39 A 723 VAL ASN THR LEU VAL GLU PHE ALA ARG ARG ALA GLY VAL SEQRES 40 A 723 ASP PRO GLN LEU VAL ASN PHE ARG ASN ALA GLU ASP VAL SEQRES 41 A 723 TRP ASN GLU TRP ARG MET VAL SER LYS GLY THR THR TYR SEQRES 42 A 723 ASP PHE TRP GLY MET THR ARG GLU ARG LEU ARG LYS GLU SEQRES 43 A 723 SER GLY LEU ILE TRP PRO CYS PRO SER GLU ASP HIS PRO SEQRES 44 A 723 GLY THR SER LEU ARG TYR VAL ARG GLY GLN ASP PRO CYS SEQRES 45 A 723 VAL PRO ALA ASP HIS PRO ASP ARG PHE PHE PHE TYR GLY SEQRES 46 A 723 LYS PRO ASP GLY ARG ALA VAL ILE TRP MET ARG PRO ALA SEQRES 47 A 723 LYS GLY ALA ALA GLU GLU PRO ASP ALA GLU TYR PRO LEU SEQRES 48 A 723 TYR LEU THR SER MET ARG VAL ILE ASP HIS TRP HIS THR SEQRES 49 A 723 ALA THR MET THR GLY LYS VAL PRO GLU LEU GLN LYS ALA SEQRES 50 A 723 ASN PRO ILE ALA PHE VAL GLU ILE ASN GLU GLU ASP ALA SEQRES 51 A 723 ALA ARG THR GLY ILE LYS HIS GLY ASP SER VAL ILE VAL SEQRES 52 A 723 GLU THR ARG ARG ASP ALA MET GLU LEU PRO ALA ARG VAL SEQRES 53 A 723 SER ASP VAL CYS ARG PRO GLY LEU ILE ALA VAL PRO PHE SEQRES 54 A 723 PHE ASP PRO LYS LYS LEU VAL ASN LYS LEU PHE LEU ASP SEQRES 55 A 723 ALA THR ASP PRO VAL SER ARG GLU PRO GLU TYR LYS ILE SEQRES 56 A 723 CYS ALA ALA ARG VAL ARG LYS ALA HET SF4 A 800 8 HET MO A 810 1 HET MGD A 811 47 HET MGD A 812 47 HET MES A2300 12 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM MO MOLYBDENUM ATOM HETNAM MGD 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8- HETNAM 2 MGD OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE HETNAM 3 MGD DINUCLEOTIDE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN MGD MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE FORMUL 2 SF4 FE4 S4 FORMUL 3 MO MO FORMUL 4 MGD 2(C20 H26 N10 O13 P2 S2) FORMUL 6 MES C6 H13 N O4 S FORMUL 7 HOH *595(H2 O) HELIX 1 1 LEU A 48 SER A 51 1 4 HELIX 2 2 ILE A 54 LEU A 57 1 4 HELIX 3 3 TRP A 81 TYR A 99 1 19 HELIX 4 4 PRO A 101 SER A 103 5 3 HELIX 5 5 THR A 114 GLY A 126 1 13 HELIX 6 6 ASN A 136 LEU A 139 5 4 HELIX 7 7 ALA A 142 PHE A 152 1 11 HELIX 8 8 TYR A 161 ASP A 165 5 5 HELIX 9 9 THR A 177 ALA A 180 1 4 HELIX 10 10 PRO A 182 VAL A 194 1 13 HELIX 11 11 ASN A 209 ILE A 213 5 5 HELIX 12 12 ASP A 225 ASN A 238 1 14 HELIX 13 13 PRO A 244 TYR A 250 1 7 HELIX 14 14 PHE A 263 TYR A 273 1 11 HELIX 15 15 PRO A 275 CYS A 282 1 8 HELIX 16 16 VAL A 286 GLU A 298 1 13 HELIX 17 17 GLY A 316 THR A 330 1 15 HELIX 18 18 ALA A 349 GLY A 352 1 4 HELIX 19 19 ALA A 372 TRP A 382 1 11 HELIX 20 20 THR A 397 ARG A 406 1 10 HELIX 21 21 PRO A 419 THR A 422 1 4 HELIX 22 22 LEU A 426 SER A 434 1 9 HELIX 23 23 VAL A 450 GLU A 453 5 4 HELIX 24 24 TRP A 464 GLU A 466 5 3 HELIX 25 25 THR A 494 ALA A 505 1 12 HELIX 26 26 ALA A 517 SER A 528 1 12 HELIX 27 27 ARG A 540 LYS A 545 1 6 HELIX 28 28 THR A 628 LYS A 630 5 3 HELIX 29 29 PRO A 632 GLN A 635 5 4 HELIX 30 30 GLU A 647 THR A 653 1 7 HELIX 31 31 VAL A 696 LYS A 698 5 3 SHEET 1 A 3 LYS A 7 VAL A 12 0 SHEET 2 A 3 GLY A 21 LYS A 27 -1 N VAL A 26 O LYS A 7 SHEET 3 A 3 LYS A 30 GLY A 36 -1 N GLN A 35 O LEU A 23 SHEET 1 B 5 VAL A 133 GLY A 135 0 SHEET 2 B 5 VAL A 104 GLY A 108 1 N TRP A 106 O ASP A 134 SHEET 3 B 5 CYS A 411 CYS A 415 1 N CYS A 411 O ALA A 105 SHEET 4 B 5 PHE A 439 ILE A 443 1 N PHE A 439 O MET A 412 SHEET 5 B 5 LEU A 457 LEU A 459 1 N LEU A 457 O CYS A 442 SHEET 1 C 5 THR A 339 SER A 342 0 SHEET 2 C 5 THR A 302 TRP A 306 1 N SER A 304 O THR A 339 SHEET 3 C 5 CYS A 169 ILE A 173 1 N CYS A 169 O MET A 303 SHEET 4 C 5 LYS A 199 ALA A 203 1 N LYS A 199 O PHE A 170 SHEET 5 C 5 MET A 216 VAL A 218 1 N MET A 216 O VAL A 202 SHEET 1 D 2 VAL A 251 MET A 254 0 SHEET 2 D 2 ALA A 591 TRP A 594 1 N ALA A 591 O ASN A 252 SHEET 1 E 2 GLY A 469 GLY A 472 0 SHEET 2 E 2 TYR A 478 THR A 481 -1 N THR A 481 O GLY A 469 SHEET 1 F 7 CYS A 716 ALA A 718 0 SHEET 2 F 7 LEU A 611 MET A 616 -1 N LEU A 613 O CYS A 716 SHEET 3 F 7 LEU A 684 PRO A 688 1 N ILE A 685 O TYR A 612 SHEET 4 F 7 PHE A 642 ASN A 646 -1 N GLU A 644 O ALA A 686 SHEET 5 F 7 ASP A 668 SER A 677 1 N PRO A 673 O VAL A 643 SHEET 6 F 7 SER A 660 THR A 665 -1 N THR A 665 O ASP A 668 SHEET 7 F 7 ARG A 719 LYS A 722 -1 N ARG A 721 O ILE A 662 LINK SG CYS A 13 FE4 SF4 A 800 1555 1555 2.33 LINK SG CYS A 16 FE3 SF4 A 800 1555 1555 2.33 LINK SG CYS A 20 FE2 SF4 A 800 1555 1555 2.21 LINK SG CYS A 47 FE1 SF4 A 800 1555 1555 2.32 LINK SG CYS A 140 MO MO A 810 1555 1555 2.59 LINK MO MO A 810 S12 MGD A 811 1555 1555 2.36 LINK MO MO A 810 S13 MGD A 811 1555 1555 2.19 LINK MO MO A 810 S13 MGD A 812 1555 1555 2.40 LINK MO MO A 810 S12 MGD A 812 1555 1555 2.40 LINK MO MO A 810 O HOH A 813 1555 1555 2.06 CISPEP 1 TRP A 551 PRO A 552 0 0.51 SITE 1 FS4 1 SF4 A 800 SITE 1 MGD 3 MO A 810 MGD A 811 MGD A 812 SITE 1 AC1 7 CYS A 13 TYR A 15 CYS A 16 GLY A 19 SITE 2 AC1 7 CYS A 20 CYS A 47 VAL A 183 SITE 1 AC2 4 CYS A 140 MGD A 811 MGD A 812 HOH A 813 SITE 1 AC3 33 ARG A 14 GLN A 111 ASN A 136 CYS A 140 SITE 2 AC3 33 GLN A 312 GLU A 416 THR A 417 ASN A 418 SITE 3 AC3 33 THR A 422 ILE A 443 GLU A 444 ALA A 445 SITE 4 AC3 33 PHE A 446 ALA A 449 PRO A 461 ALA A 462 SITE 5 AC3 33 PHE A 463 SER A 615 ARG A 617 TRP A 622 SITE 6 AC3 33 HIS A 623 THR A 624 THR A 626 MET A 627 SITE 7 AC3 33 PHE A 689 ASN A 697 TYR A 713 LYS A 714 SITE 8 AC3 33 MO A 810 MGD A 812 HOH A1181 HOH A1249 SITE 9 AC3 33 HOH A1507 SITE 1 AC4 36 CYS A 16 LYS A 49 CYS A 140 ILE A 173 SITE 2 AC4 36 GLY A 174 SER A 175 ASN A 176 GLU A 179 SITE 3 AC4 36 ALA A 180 ASP A 204 PRO A 205 ARG A 206 SITE 4 AC4 36 PHE A 220 PRO A 222 GLY A 223 ASP A 225 SITE 5 AC4 36 CYS A 307 MET A 308 GLY A 309 ARG A 313 SITE 6 AC4 36 GLY A 345 THR A 614 MET A 616 ARG A 617 SITE 7 AC4 36 VAL A 618 ILE A 619 HIS A 621 TRP A 622 SITE 8 AC4 36 HIS A 623 LYS A 714 MO A 810 MGD A 811 SITE 9 AC4 36 HOH A1074 HOH A1099 HOH A1150 HOH A1251 SITE 1 AC5 13 ALA A 142 VAL A 145 GLY A 146 VAL A 149 SITE 2 AC5 13 THR A 150 HIS A 361 VAL A 707 SER A 708 SITE 3 AC5 13 HOH A1096 HOH A1276 HOH A1347 HOH A1456 SITE 4 AC5 13 HOH A1542 CRYST1 106.260 106.260 134.910 90.00 90.00 120.00 P 31 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 0.009411 0.005433 0.000000 0.00000 SCALE2 0.000000 0.010867 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007412 0.00000