HEADER IRON PROTEIN 29-SEP-92 1NIP TITLE CRYSTALLOGRAPHIC STRUCTURE OF THE NITROGENASE IRON PROTEIN FROM TITLE 2 AZOTOBACTER VINELANDII CAVEAT 1NIP CHIRALITY ERROR AT CA IN RESIDUES 43, 84 AND 191 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROGENASE IRON PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AZOTOBACTER VINELANDII; SOURCE 3 ORGANISM_TAXID: 354 KEYWDS IRON PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.KOMIYA,M.M.GEORGIADIS,P.CHAKRABARTI,D.WOO,J.J.KORNUC,D.C.REES REVDAT 4 14-FEB-24 1NIP 1 REMARK LINK REVDAT 3 24-MAR-09 1NIP 1 ATOM CONECT REVDAT 2 24-FEB-09 1NIP 1 VERSN REVDAT 1 31-OCT-93 1NIP 0 JRNL AUTH M.M.GEORGIADIS,H.KOMIYA,P.CHAKRABARTI,D.WOO,J.J.KORNUC, JRNL AUTH 2 D.C.REES JRNL TITL CRYSTALLOGRAPHIC STRUCTURE OF THE NITROGENASE IRON PROTEIN JRNL TITL 2 FROM AZOTOBACTER VINELANDII. JRNL REF SCIENCE V. 257 1653 1992 JRNL REFN ISSN 0036-8075 JRNL PMID 1529353 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.M.GEORGIADIS,P.CHAKRABARTI,D.C.REES REMARK 1 TITL CRYSTAL STRUCTURE OF THE NITROGENASE IRON PROTEIN FROM REMARK 1 TITL 2 AZOTOBACTER VINELANDII REMARK 1 EDIT P.M.GRESSHOFF, L.E.ROTH, G.STACEY, W.E.NEWTON REMARK 1 REF NITROGEN FIXATION: 1 1990 REMARK 1 REF 2 ACHIEVEMENTS AND OBJECTIVES REMARK 1 PUBL CHAPMAN AND HALL, NEW YORK REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4110 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.017 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.231 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THERE ARE NO RELIABLE POSITIONS FROM A 284 TO A 289 AND REMARK 3 FROM B 288 TO B 289. REMARK 3 REMARK 3 THE ADP COORDINATES ARE NOT AS RELIABLE AS OTHER ATOMS REMARK 3 DUE TO THE LOW OCCUPANCY. ITS TEMPERATURE FACTOR REMARK 3 AND OCCUPANCY WERE FIXED TO 29.0 AND 0.5, RESPECTIVELY, REMARK 3 DURING REFINEMENT. REMARK 4 REMARK 4 1NIP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175306. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 46.45000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 LYS A 284 REMARK 465 THR A 285 REMARK 465 ALA A 286 REMARK 465 GLU A 287 REMARK 465 GLU A 288 REMARK 465 VAL A 289 REMARK 465 GLU B 288 REMARK 465 VAL B 289 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 LYS A 32 CG CD CE NZ REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 GLU A 63 CG CD OE1 OE2 REMARK 470 GLU A 68 CG CD OE1 OE2 REMARK 470 LEU A 70 CG CD1 CD2 REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 LYS A 77 CG CD CE NZ REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 GLU A 116 CD OE1 OE2 REMARK 470 ASP A 118 CG OD1 OD2 REMARK 470 LYS A 170 CD CE NZ REMARK 470 ARG A 187 CD NE CZ NH1 NH2 REMARK 470 ARG A 191 NE CZ NH1 NH2 REMARK 470 GLU A 194 CG CD OE1 OE2 REMARK 470 LYS A 202 CD CE NZ REMARK 470 ASN A 215 CG OD1 ND2 REMARK 470 GLN A 218 CG CD OE1 NE2 REMARK 470 LYS A 233 CG CD CE NZ REMARK 470 LYS A 235 CG CD CE NZ REMARK 470 ARG A 245 CD NE CZ NH1 NH2 REMARK 470 LYS A 251 CD CE NZ REMARK 470 GLU A 265 CG CD OE1 OE2 REMARK 470 MET A 269 SD CE REMARK 470 GLU A 275 CG CD OE1 OE2 REMARK 470 ASP A 278 CG OD1 OD2 REMARK 470 LYS B 32 CG CD CE NZ REMARK 470 LEU B 49 CG CD1 CD2 REMARK 470 LYS B 52 CG CD CE NZ REMARK 470 GLU B 63 CD OE1 OE2 REMARK 470 VAL B 67 CG1 CG2 REMARK 470 GLU B 68 CG CD OE1 OE2 REMARK 470 ASP B 69 OD1 OD2 REMARK 470 LEU B 70 CG CD1 CD2 REMARK 470 GLU B 71 CG CD OE1 OE2 REMARK 470 GLU B 73 OE1 OE2 REMARK 470 LYS B 77 CE NZ REMARK 470 LYS B 84 CD CE NZ REMARK 470 GLU B 111 CD OE1 OE2 REMARK 470 GLU B 116 CG CD OE1 OE2 REMARK 470 ASP B 118 CG OD1 OD2 REMARK 470 LEU B 119 CG CD1 CD2 REMARK 470 ASN B 142 CG OD1 ND2 REMARK 470 LYS B 143 CE NZ REMARK 470 ASN B 173 CG OD1 ND2 REMARK 470 SER B 174 OG REMARK 470 ARG B 187 CD NE CZ NH1 NH2 REMARK 470 ARG B 219 CD NE CZ NH1 NH2 REMARK 470 LYS B 233 CE NZ REMARK 470 LYS B 235 CD CE NZ REMARK 470 ARG B 245 CD NE CZ NH1 NH2 REMARK 470 LYS B 251 CD CE NZ REMARK 470 GLU B 266 CG CD OE1 OE2 REMARK 470 GLU B 270 CD OE1 OE2 REMARK 470 PHE B 271 CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 275 CG CD OE1 OE2 REMARK 470 ILE B 281 CD1 REMARK 470 LYS B 284 CG CD CE NZ REMARK 470 THR B 285 OG1 CG2 REMARK 470 GLU B 287 CG CD OE1 OE2 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 VAL A 169 N ALA A 172 2.07 REMARK 500 N GLY A 12 O1B ADP B 292 2.10 REMARK 500 O ALA A 172 N GLY A 175 2.13 REMARK 500 O VAL A 169 N TYR A 171 2.14 REMARK 500 O GLU B 221 N ARG B 224 2.14 REMARK 500 OD1 ASP A 238 NH1 ARG A 241 2.15 REMARK 500 O ILE A 57 N MET A 60 2.18 REMARK 500 O MET B 156 N TYR B 159 2.18 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 GLU A 73 CD GLU A 73 OE2 0.076 REMARK 500 GLU A 112 CD GLU A 112 OE2 0.101 REMARK 500 GLU A 141 CD GLU A 141 OE2 0.069 REMARK 500 GLU A 146 CD GLU A 146 OE1 0.072 REMARK 500 GLU A 192 CD GLU A 192 OE1 0.068 REMARK 500 GLU A 229 CD GLU A 229 OE1 0.072 REMARK 500 GLU A 270 CD GLU A 270 OE1 0.067 REMARK 500 GLU B 87 CD GLU B 87 OE1 0.077 REMARK 500 GLU B 279 CD GLU B 279 OE2 0.072 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 69 CB - CG - OD1 ANGL. DEV. = -7.6 DEGREES REMARK 500 ASP A 69 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 74 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 74 CB - CG - OD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ASP A 120 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 125 CB - CG - OD1 ANGL. DEV. = -9.5 DEGREES REMARK 500 ASP A 125 CB - CG - OD2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP A 129 CB - CG - OD1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 129 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 190 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 193 CB - CG - OD1 ANGL. DEV. = -6.7 DEGREES REMARK 500 PRO A 212 C - N - CD ANGL. DEV. = -12.8 DEGREES REMARK 500 ASP A 214 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 214 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 231 CB - CG - OD1 ANGL. DEV. = -7.4 DEGREES REMARK 500 ASP A 238 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 241 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 249 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 249 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 262 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP B 39 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP B 117 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP B 120 CB - CG - OD1 ANGL. DEV. = -8.5 DEGREES REMARK 500 ASP B 125 CB - CG - OD1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP B 129 CB - CG - OD1 ANGL. DEV. = -6.1 DEGREES REMARK 500 ASP B 129 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 193 CB - CG - OD1 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP B 193 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 PRO B 256 C - N - CD ANGL. DEV. = -22.0 DEGREES REMARK 500 ASP B 262 CB - CG - OD2 ANGL. DEV. = -6.4 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 VAL A 23 -28.75 -39.49 REMARK 500 SER A 44 -80.60 -11.76 REMARK 500 ARG A 46 -69.67 164.06 REMARK 500 ALA A 53 121.94 -172.04 REMARK 500 ASP A 69 -78.52 -71.81 REMARK 500 LEU A 70 117.19 -13.88 REMARK 500 LEU A 72 -64.82 -12.22 REMARK 500 GLU A 73 -73.55 -36.37 REMARK 500 ASP A 74 -19.83 -38.13 REMARK 500 SER A 88 -70.83 -46.37 REMARK 500 GLU A 92 113.47 -34.94 REMARK 500 PRO A 93 139.84 -36.46 REMARK 500 ILE A 103 -78.05 -37.13 REMARK 500 THR A 104 -50.10 -18.24 REMARK 500 GLU A 116 -105.31 -83.50 REMARK 500 ASP A 117 44.72 19.21 REMARK 500 ASP A 118 84.75 47.30 REMARK 500 CYS A 132 -169.15 -125.24 REMARK 500 MET A 137 -72.22 -30.45 REMARK 500 ILE A 139 -88.16 -77.82 REMARK 500 ARG A 140 -36.65 -38.05 REMARK 500 GLU A 141 38.80 -96.11 REMARK 500 ASN A 142 75.55 9.34 REMARK 500 MET A 155 -40.36 -14.83 REMARK 500 LYS A 166 -28.63 -39.36 REMARK 500 VAL A 169 -89.52 -46.71 REMARK 500 LYS A 170 -45.24 -9.78 REMARK 500 ALA A 172 -77.37 -69.88 REMARK 500 ASN A 173 -35.80 -35.72 REMARK 500 SER A 176 16.04 106.00 REMARK 500 ARG A 191 12.91 -146.91 REMARK 500 GLU A 192 -79.80 -37.73 REMARK 500 ASP A 193 -58.09 -10.73 REMARK 500 LEU A 195 -75.49 -39.89 REMARK 500 LEU A 199 -71.01 -48.94 REMARK 500 ALA A 200 -57.03 -28.89 REMARK 500 ILE A 208 -40.99 -19.11 REMARK 500 ARG A 213 45.52 -109.29 REMARK 500 ASN A 215 -18.43 -39.54 REMARK 500 VAL A 217 -72.08 -66.77 REMARK 500 TYR A 230 -125.11 -57.61 REMARK 500 LYS A 233 43.75 -87.33 REMARK 500 ASP A 249 -74.73 -110.97 REMARK 500 ASN A 250 107.10 -4.91 REMARK 500 GLU A 266 -60.62 -23.40 REMARK 500 MET A 269 -71.39 -64.59 REMARK 500 GLU A 270 -56.25 -21.22 REMARK 500 ILE A 273 -80.16 -23.69 REMARK 500 GLU A 275 -168.06 -57.56 REMARK 500 VAL A 276 139.55 -39.79 REMARK 500 REMARK 500 THIS ENTRY HAS 104 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR B 80 0.07 SIDE CHAIN 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 ASP A 129 -10.59 REMARK 500 ILE A 139 -11.28 REMARK 500 MET A 269 -11.03 REMARK 500 ALA B 200 -11.40 REMARK 500 GLN B 206 -11.28 REMARK 500 VAL B 282 14.99 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 MG A 291 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 16 OG REMARK 620 2 HOH A5011 O 82.6 REMARK 620 3 HOH A5013 O 60.3 110.8 REMARK 620 4 ADP B 292 O3B 119.5 135.2 114.1 REMARK 620 5 HOH B5012 O 167.2 108.2 108.4 57.6 REMARK 620 6 HOH B5014 O 67.4 106.0 109.0 58.5 114.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 290 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 97 SG REMARK 620 2 SF4 B 290 S1 73.2 REMARK 620 3 SF4 B 290 S2 116.9 105.3 REMARK 620 4 SF4 B 290 S4 138.8 105.3 103.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 290 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 132 SG REMARK 620 2 SF4 B 290 S1 129.8 REMARK 620 3 SF4 B 290 S3 111.9 104.5 REMARK 620 4 SF4 B 290 S4 98.9 105.5 102.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 291 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 16 OG REMARK 620 2 HOH B5025 O 56.5 REMARK 620 3 HOH B5026 O 122.2 109.0 REMARK 620 4 HOH B5027 O 127.3 109.5 110.5 REMARK 620 5 HOH B5028 O 51.0 107.3 111.6 108.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 290 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 97 SG REMARK 620 2 SF4 B 290 S2 79.3 REMARK 620 3 SF4 B 290 S3 139.8 105.3 REMARK 620 4 SF4 B 290 S4 113.8 102.2 104.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 290 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 132 SG REMARK 620 2 SF4 B 290 S1 115.9 REMARK 620 3 SF4 B 290 S2 124.0 106.4 REMARK 620 4 SF4 B 290 S3 97.3 106.0 104.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: FES REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: THE 4S-FE CLUSTER REMARK 800 REMARK 800 SITE_IDENTIFIER: WMA REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: WALKER A MOTIF REMARK 800 REMARK 800 SITE_IDENTIFIER: WMB REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: WALKER B MOTIF REMARK 800 REMARK 800 SITE_IDENTIFIER: ATP REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: A POSSIBLE SITE FOR ATP HYDROLYSIS REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 291 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 291 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 B 290 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 292 DBREF 1NIP A 1 289 UNP P00459 NIFH1_AZOVI 1 289 DBREF 1NIP B 1 289 UNP P00459 NIFH1_AZOVI 1 289 SEQRES 1 A 289 ALA MET ARG GLN CYS ALA ILE TYR GLY LYS GLY GLY ILE SEQRES 2 A 289 GLY LYS SER THR THR THR GLN ASN LEU VAL ALA ALA LEU SEQRES 3 A 289 ALA GLU MET GLY LYS LYS VAL MET ILE VAL GLY CYS ASP SEQRES 4 A 289 PRO LYS ALA ASP SER THR ARG LEU ILE LEU HIS SER LYS SEQRES 5 A 289 ALA GLN ASN THR ILE MET GLU MET ALA ALA GLU ALA GLY SEQRES 6 A 289 THR VAL GLU ASP LEU GLU LEU GLU ASP VAL LEU LYS ALA SEQRES 7 A 289 GLY TYR GLY GLY VAL LYS CYS VAL GLU SER GLY GLY PRO SEQRES 8 A 289 GLU PRO GLY VAL GLY CYS ALA GLY ARG GLY VAL ILE THR SEQRES 9 A 289 ALA ILE ASN PHE LEU GLU GLU GLU GLY ALA TYR GLU ASP SEQRES 10 A 289 ASP LEU ASP PHE VAL PHE TYR ASP VAL LEU GLY ASP VAL SEQRES 11 A 289 VAL CYS GLY GLY PHE ALA MET PRO ILE ARG GLU ASN LYS SEQRES 12 A 289 ALA GLN GLU ILE TYR ILE VAL CYS SER GLY GLU MET MET SEQRES 13 A 289 ALA MET TYR ALA ALA ASN ASN ILE SER LYS GLY ILE VAL SEQRES 14 A 289 LYS TYR ALA ASN SER GLY SER VAL ARG LEU GLY GLY LEU SEQRES 15 A 289 ILE CYS ASN SER ARG ASN THR ASP ARG GLU ASP GLU LEU SEQRES 16 A 289 ILE ILE ALA LEU ALA ASN LYS LEU GLY THR GLN MET ILE SEQRES 17 A 289 HIS PHE VAL PRO ARG ASP ASN VAL VAL GLN ARG ALA GLU SEQRES 18 A 289 ILE ARG ARG MET THR VAL ILE GLU TYR ASP PRO LYS ALA SEQRES 19 A 289 LYS GLN ALA ASP GLU TYR ARG ALA LEU ALA ARG LYS VAL SEQRES 20 A 289 VAL ASP ASN LYS LEU LEU VAL ILE PRO ASN PRO ILE THR SEQRES 21 A 289 MET ASP GLU LEU GLU GLU LEU LEU MET GLU PHE GLY ILE SEQRES 22 A 289 MET GLU VAL GLU ASP GLU SER ILE VAL GLY LYS THR ALA SEQRES 23 A 289 GLU GLU VAL SEQRES 1 B 289 ALA MET ARG GLN CYS ALA ILE TYR GLY LYS GLY GLY ILE SEQRES 2 B 289 GLY LYS SER THR THR THR GLN ASN LEU VAL ALA ALA LEU SEQRES 3 B 289 ALA GLU MET GLY LYS LYS VAL MET ILE VAL GLY CYS ASP SEQRES 4 B 289 PRO LYS ALA ASP SER THR ARG LEU ILE LEU HIS SER LYS SEQRES 5 B 289 ALA GLN ASN THR ILE MET GLU MET ALA ALA GLU ALA GLY SEQRES 6 B 289 THR VAL GLU ASP LEU GLU LEU GLU ASP VAL LEU LYS ALA SEQRES 7 B 289 GLY TYR GLY GLY VAL LYS CYS VAL GLU SER GLY GLY PRO SEQRES 8 B 289 GLU PRO GLY VAL GLY CYS ALA GLY ARG GLY VAL ILE THR SEQRES 9 B 289 ALA ILE ASN PHE LEU GLU GLU GLU GLY ALA TYR GLU ASP SEQRES 10 B 289 ASP LEU ASP PHE VAL PHE TYR ASP VAL LEU GLY ASP VAL SEQRES 11 B 289 VAL CYS GLY GLY PHE ALA MET PRO ILE ARG GLU ASN LYS SEQRES 12 B 289 ALA GLN GLU ILE TYR ILE VAL CYS SER GLY GLU MET MET SEQRES 13 B 289 ALA MET TYR ALA ALA ASN ASN ILE SER LYS GLY ILE VAL SEQRES 14 B 289 LYS TYR ALA ASN SER GLY SER VAL ARG LEU GLY GLY LEU SEQRES 15 B 289 ILE CYS ASN SER ARG ASN THR ASP ARG GLU ASP GLU LEU SEQRES 16 B 289 ILE ILE ALA LEU ALA ASN LYS LEU GLY THR GLN MET ILE SEQRES 17 B 289 HIS PHE VAL PRO ARG ASP ASN VAL VAL GLN ARG ALA GLU SEQRES 18 B 289 ILE ARG ARG MET THR VAL ILE GLU TYR ASP PRO LYS ALA SEQRES 19 B 289 LYS GLN ALA ASP GLU TYR ARG ALA LEU ALA ARG LYS VAL SEQRES 20 B 289 VAL ASP ASN LYS LEU LEU VAL ILE PRO ASN PRO ILE THR SEQRES 21 B 289 MET ASP GLU LEU GLU GLU LEU LEU MET GLU PHE GLY ILE SEQRES 22 B 289 MET GLU VAL GLU ASP GLU SER ILE VAL GLY LYS THR ALA SEQRES 23 B 289 GLU GLU VAL HET MG A 291 1 HET MG B 291 1 HET SF4 B 290 8 HET ADP B 292 27 HETNAM MG MAGNESIUM ION HETNAM SF4 IRON/SULFUR CLUSTER HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 3 MG 2(MG 2+) FORMUL 5 SF4 FE4 S4 FORMUL 6 ADP C10 H15 N5 O10 P2 FORMUL 7 HOH *17(H2 O) HELIX 1 1 GLY A 14 MET A 29 1 16 HELIX 2 2 THR A 56 GLY A 65 1 10 HELIX 3 3 GLU A 71 LEU A 76 1 6 HELIX 4 4 TYR A 80 GLY A 82 5 3 HELIX 5 5 CYS A 97 GLU A 112 1 16 HELIX 6 6 LEU A 127 VAL A 131 5 5 HELIX 7 7 CYS A 132 PHE A 135 5 4 HELIX 8 8 ALA A 136 GLU A 141 1 6 HELIX 9 9 MET A 158 TYR A 171 1 14 HELIX 10 10 ARG A 191 GLY A 204 1 14 HELIX 11 11 ASN A 215 ILE A 222 1 8 HELIX 12 12 ALA A 234 ASN A 250 1 17 HELIX 13 13 THR A 260 GLY A 272 1 13 HELIX 14 14 GLY B 14 GLY B 30 1 17 HELIX 15 15 THR B 56 GLY B 65 1 10 HELIX 16 16 GLU B 71 LEU B 76 1 6 HELIX 17 17 GLY B 79 VAL B 83 5 5 HELIX 18 18 CYS B 97 GLU B 112 1 16 HELIX 19 19 CYS B 132 GLU B 141 1 10 HELIX 20 20 GLU B 154 ASN B 173 1 20 HELIX 21 21 ARG B 191 GLY B 204 1 14 HELIX 22 22 ASN B 215 ILE B 222 1 8 HELIX 23 23 THR B 226 ASP B 231 1 6 HELIX 24 24 ALA B 234 ASN B 250 1 17 HELIX 25 25 THR B 260 GLY B 272 1 13 SHEET 1 A 8 LYS A 77 GLY A 79 0 SHEET 2 A 8 VAL A 83 GLU A 87 -1 O VAL A 83 N GLY A 79 SHEET 3 A 8 VAL A 33 GLY A 37 1 O VAL A 33 N LYS A 84 SHEET 4 A 8 PHE A 121 ASP A 125 1 O PHE A 121 N MET A 34 SHEET 5 A 8 ARG A 3 TYR A 8 1 O ARG A 3 N VAL A 122 SHEET 6 A 8 GLU A 146 CYS A 151 1 O GLU A 146 N ALA A 6 SHEET 7 A 8 ARG A 178 ASN A 185 1 O ARG A 178 N ILE A 147 SHEET 8 A 8 HIS A 209 VAL A 211 1 O HIS A 209 N CYS A 184 SHEET 1 B 6 LYS B 84 GLU B 87 0 SHEET 2 B 6 VAL B 33 GLY B 37 1 O VAL B 33 N LYS B 84 SHEET 3 B 6 PHE B 121 ASP B 125 1 O PHE B 121 N MET B 34 SHEET 4 B 6 ARG B 3 ILE B 7 1 O ARG B 3 N VAL B 122 SHEET 5 B 6 GLU B 146 TYR B 148 1 O GLU B 146 N ALA B 6 SHEET 6 B 6 ARG B 178 LEU B 179 1 O ARG B 178 N ILE B 147 SHEET 1 C 2 GLY B 181 ASN B 185 0 SHEET 2 C 2 GLN B 206 VAL B 211 1 O GLN B 206 N LEU B 182 LINK OG SER A 16 MG MG A 291 1555 1555 2.63 LINK SG CYS A 97 FE3 SF4 B 290 1555 1555 2.30 LINK SG CYS A 132 FE2 SF4 B 290 1555 1555 2.30 LINK MG MG A 291 O HOH A5011 1555 1555 1.80 LINK MG MG A 291 O HOH A5013 1555 1555 1.79 LINK MG MG A 291 O3B ADP B 292 1555 1555 2.57 LINK MG MG A 291 O HOH B5012 1555 1555 1.79 LINK MG MG A 291 O HOH B5014 1555 1555 1.79 LINK OG SER B 16 MG MG B 291 1555 1555 2.87 LINK SG CYS B 97 FE1 SF4 B 290 1555 1555 2.26 LINK SG CYS B 132 FE4 SF4 B 290 1555 1555 2.32 LINK MG MG B 291 O HOH B5025 1555 1555 1.80 LINK MG MG B 291 O HOH B5026 1555 1555 1.81 LINK MG MG B 291 O HOH B5027 1555 1555 1.79 LINK MG MG B 291 O HOH B5028 1555 1555 1.77 SITE 1 FES 4 CYS A 97 CYS A 132 CYS B 97 CYS B 132 SITE 1 WMA 16 GLY A 9 LYS A 10 GLY A 11 GLY A 12 SITE 2 WMA 16 ILE A 13 GLY A 14 LYS A 15 SER A 16 SITE 3 WMA 16 GLY B 9 LYS B 10 GLY B 11 GLY B 12 SITE 4 WMA 16 ILE B 13 GLY B 14 LYS B 15 SER B 16 SITE 1 WMB 2 ASP A 125 ASP B 125 SITE 1 ATP 4 ASP A 39 ASP A 43 ASP B 39 ASP B 43 SITE 1 AC1 7 GLY A 14 SER A 16 HOH A5011 HOH A5013 SITE 2 AC1 7 ADP B 292 HOH B5012 HOH B5014 SITE 1 AC2 6 GLY B 14 SER B 16 HOH B5025 HOH B5026 SITE 2 AC2 6 HOH B5027 HOH B5028 SITE 1 AC3 10 CYS A 97 ALA A 98 CYS A 132 GLY A 133 SITE 2 AC3 10 GLY A 134 CYS B 97 ALA B 98 CYS B 132 SITE 3 AC3 10 GLY B 134 PHE B 135 SITE 1 AC4 16 GLY A 11 GLY A 12 ILE A 13 LYS A 41 SITE 2 AC4 16 ALA A 42 MG A 291 HOH A5013 LYS B 10 SITE 3 AC4 16 GLY B 11 GLY B 128 ASP B 129 MET B 156 SITE 4 AC4 16 ALA B 160 HOH B 298 HOH B5012 HOH B5014 CRYST1 56.800 92.900 63.600 90.00 100.00 90.00 P 1 21 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 0.017606 0.000000 0.003104 0.00000 SCALE2 0.000000 0.010764 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015966 0.00000