HEADER OXIDOREDUCTASE 08-DEC-05 2C8V TITLE INSIGHTS INTO THE ROLE OF NUCLEOTIDE-DEPENDENT CONFORMATIONAL CHANGE TITLE 2 IN NITROGENASE CATALYSIS: STRUCTURAL CHARACTERIZATION OF THE TITLE 3 NITROGENASE FE PROTEIN LEU127 DELETION VARIANT WITH BOUND MGATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROGENASE IRON PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NITROGENASE COMPONENT II, NITROGENASE REDUCTASE, NIFH, AV2, COMPND 5 NITROGENASE FE PROTEIN 1; COMPND 6 EC: 1.18.6.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AZOTOBACTER VINELANDII; SOURCE 3 ORGANISM_TAXID: 354 KEYWDS OXIDOREDUCTASE, NITROGENASE, NITROGEN FIXATION, MGADP, FE PROTEIN, KEYWDS 2 AV2, 4FE- 4S, ATP-BINDING, IRON, IRON-SULFUR, METAL-BINDING, KEYWDS 3 NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.SEN,A.KRISHNAKUMAR,J.MCCLEAD,M.K.JOHNSON,L.C.SEEFELDT,R.K.SZILAGYI, AUTHOR 2 J.W.PETERS REVDAT 5 08-MAY-24 2C8V 1 REMARK LINK REVDAT 4 27-MAR-13 2C8V 1 REMARK VERSN HET HETNAM REVDAT 4 2 1 FORMUL LINK SITE HETATM REVDAT 3 24-FEB-09 2C8V 1 VERSN REVDAT 2 16-OCT-06 2C8V 1 CONECT REVDAT 1 01-JUN-06 2C8V 0 JRNL AUTH S.SEN,A.KRISHNAKUMAR,J.MCCLEAD,M.K.JOHNSON,L.C.SEEFELDT, JRNL AUTH 2 R.K.SZILAGYI,J.W.PETERS JRNL TITL INSIGHTS INTO THE ROLE OF NUCLEOTIDE-DEPENDENT JRNL TITL 2 CONFORMATIONAL CHANGE IN NITROGENASE CATALYSIS: STRUCTURAL JRNL TITL 3 CHARACTERIZATION OF THE NITROGENASE FE PROTEIN LEU127 JRNL TITL 4 DELETION VARIANT WITH BOUND MGATP. JRNL REF J.INORG.BIOCHEM. V. 100 1041 2006 JRNL REFN ISSN 0162-0134 JRNL PMID 16616373 JRNL DOI 10.1016/J.JINORGBIO.2006.02.016 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.500 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 22950 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) : 0.238 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 2050 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 99 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) : 2.520 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 2C8V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1290026739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 93.0 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : FLAT MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BLU-ICE, DENZO REMARK 200 DATA SCALING SOFTWARE : MOSFLM, SCALEPACK, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20818 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.07900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% POLY(ETHYLENE GLYCOL), MW 4000, REMARK 280 0.16 M MGCL2, TRISHYDROCHLORIC ACID, PH 8.5, 20% GLYCEROL, AND REMARK 280 1MM SODIUM DITHIONITE, PH 8.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 30.75000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.75000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.45000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 66.65000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.45000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 66.65000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.75000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.45000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.65000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.75000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.45000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 66.65000 REMARK 290 SMTRY3 8 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: 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 400 REMARK 400 COMPOUND REMARK 400 DELETION MUTANT LEU 127. 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 274 REMARK 465 GLU A 275 REMARK 465 VAL A 276 REMARK 465 GLU A 277 REMARK 465 ASP A 278 REMARK 465 GLU A 279 REMARK 465 SER A 280 REMARK 465 ILE A 281 REMARK 465 VAL A 282 REMARK 465 GLY A 283 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 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 ILE A 273 CA C O CB CG1 CG2 CD1 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 S1 FES A 290 FE1 FES A 291 4555 2.13 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 HIS A 50 NE2 HIS A 50 CD2 -0.070 REMARK 500 HIS A 209 NE2 HIS A 209 CD2 -0.071 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 3 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 3 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 LYS A 41 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 CYS A 97 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 191 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 224 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 241 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 245 NE - CZ - NH1 ANGL. DEV. = 3.1 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 MET A 2 106.79 -56.59 REMARK 500 ALA A 42 90.48 -54.33 REMARK 500 ASP A 43 20.33 -142.38 REMARK 500 ALA A 53 146.49 170.63 REMARK 500 GLU A 59 28.05 -141.66 REMARK 500 VAL A 67 -50.06 -129.43 REMARK 500 GLU A 68 17.67 -144.85 REMARK 500 ASP A 69 61.84 -105.36 REMARK 500 ALA A 98 -113.37 -76.49 REMARK 500 ALA A 105 -51.88 -153.05 REMARK 500 VAL A 126 -131.45 -88.29 REMARK 500 VAL A 131 57.29 -103.13 REMARK 500 PRO A 138 3.86 -54.71 REMARK 500 ARG A 140 178.13 -59.42 REMARK 500 LYS A 143 -149.38 -118.55 REMARK 500 LYS A 170 46.13 -100.81 REMARK 500 ALA A 172 -89.25 -32.15 REMARK 500 SER A 174 84.29 -66.85 REMARK 500 SER A 176 65.13 -168.48 REMARK 500 SER A 186 154.11 -46.83 REMARK 500 ARG A 187 -22.28 -159.89 REMARK 500 ASN A 188 -106.66 -117.01 REMARK 500 THR A 189 -129.15 -157.95 REMARK 500 THR A 205 -160.53 -109.40 REMARK 500 HIS A 209 143.29 -172.54 REMARK 500 PHE A 271 -87.94 -116.02 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 GLY A 90 PRO A 91 145.73 REMARK 500 MET A 137 PRO A 138 147.55 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 293 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 16 OG REMARK 620 2 HOH A2004 O 77.3 REMARK 620 3 HOH A2014 O 78.5 71.7 REMARK 620 4 HOH A2099 O 92.6 166.8 115.0 REMARK 620 5 ATP A5292 O1B 85.5 81.8 151.4 89.0 REMARK 620 6 ATP A5292 O3G 158.9 82.0 99.1 107.1 87.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 290 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 97 SG REMARK 620 2 FES A 290 S1 88.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 291 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 132 SG REMARK 620 2 FES A 291 S1 120.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES A 290 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES A 291 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 5292 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DE0 RELATED DB: PDB REMARK 900 MODULATING THE MIDPOINT POTENTIAL OF THE [ 4FE-4S] CLUSTEROF THE REMARK 900 NITROGENASE FE PROTEIN REMARK 900 RELATED ID: 1FP6 RELATED DB: PDB REMARK 900 THE NITROGENASE FE PROTEIN FROM AZOTOBACTER VINELANDIICOMPLEXED REMARK 900 WITH MGADP REMARK 900 RELATED ID: 1G1M RELATED DB: PDB REMARK 900 ALL-FERROUS NITROGENASE IRON PROTEIN FROM AZOTOBACTERVINELANDII REMARK 900 RELATED ID: 1G20 RELATED DB: PDB REMARK 900 MGATP-BOUND AND NUCLEOTIDE-FREE STRUCTURES OF A NITROGENASEPROTEIN REMARK 900 COMPLEX BETWEEN LEU127DEL-FE PROTEIN AND THE MOFEPROTEIN REMARK 900 RELATED ID: 1G21 RELATED DB: PDB REMARK 900 MGATP-BOUND AND NUCLEOTIDE-FREE STRUCTURES OF A NITROGENASEPROTEIN REMARK 900 COMPLEX BETWEEN LEU127DEL-FE PROTEIN AND THE MOFEPROTEIN REMARK 900 RELATED ID: 1G5P RELATED DB: PDB REMARK 900 NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII REMARK 900 RELATED ID: 1M1Y RELATED DB: PDB REMARK 900 CHEMICAL CROSSLINK OF NITROGENASE MOFE PROTEIN AND FEPROTEIN REMARK 900 RELATED ID: 1M34 RELATED DB: PDB REMARK 900 NITROGENASE COMPLEX FROM AZOTOBACTER VINELANDII STABILIZEDBY ADP- REMARK 900 TETRAFLUOROALUMINATE REMARK 900 RELATED ID: 1N2C RELATED DB: PDB REMARK 900 NITROGENASE COMPLEX FROM AZOTOBACTER VINELANDII STABILIZED BY ADP- REMARK 900 TETRAFLUOROALUMINATE REMARK 900 RELATED ID: 1NIP RELATED DB: PDB REMARK 900 RELATED ID: 1RW4 RELATED DB: PDB REMARK 900 NITROGENASE FE PROTEIN L127 DELETION VARIANT REMARK 900 RELATED ID: 1XCP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE NITROGENASE FE PROTEIN PHE135TRPWITH MGADP REMARK 900 BOUND REMARK 900 RELATED ID: 1XD8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE NITROGENASE FE PROTEIN ASP39ASN REMARK 900 RELATED ID: 1XD9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE NITROGENASE FE PROTEIN ASP39ASNWITH MGADP REMARK 900 BOUND REMARK 900 RELATED ID: 1XDB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE NITROGENASE FE PROTEIN ASP129GLU REMARK 900 RELATED ID: 2AFH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NUCLEOTIDE-FREE AV2-AV1 COMPLEX REMARK 900 RELATED ID: 2AFI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MGADP BOUND AV2-AV1 COMPLEX REMARK 900 RELATED ID: 2AFK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MGAMPPCP-BOUND AV2-AV1 COMPLEX REMARK 900 RELATED ID: 2NIP RELATED DB: PDB REMARK 900 NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE STRUCTURE BELOW DESCRIBES A DELETION MUTANT WHERE REMARK 999 RESIDUE A127 LEU HAS BEEN REMOVED. DBREF 2C8V A 1 126 UNP P00459 NIH1_AZOVI 1 126 DBREF 2C8V A 128 289 UNP P00459 NIH1_AZOVI 128 289 SEQRES 1 A 288 ALA MET ARG GLN CYS ALA ILE TYR GLY LYS GLY GLY ILE SEQRES 2 A 288 GLY LYS SER THR THR THR GLN ASN LEU VAL ALA ALA LEU SEQRES 3 A 288 ALA GLU MET GLY LYS LYS VAL MET ILE VAL GLY CYS ASP SEQRES 4 A 288 PRO LYS ALA ASP SER THR ARG LEU ILE LEU HIS SER LYS SEQRES 5 A 288 ALA GLN ASN THR ILE MET GLU MET ALA ALA GLU ALA GLY SEQRES 6 A 288 THR VAL GLU ASP LEU GLU LEU GLU ASP VAL LEU LYS ALA SEQRES 7 A 288 GLY TYR GLY GLY VAL LYS CYS VAL GLU SER GLY GLY PRO SEQRES 8 A 288 GLU PRO GLY VAL GLY CYS ALA GLY ARG GLY VAL ILE THR SEQRES 9 A 288 ALA ILE ASN PHE LEU GLU GLU GLU GLY ALA TYR GLU ASP SEQRES 10 A 288 ASP LEU ASP PHE VAL PHE TYR ASP VAL GLY ASP VAL VAL SEQRES 11 A 288 CYS GLY GLY PHE ALA MET PRO ILE ARG GLU ASN LYS ALA SEQRES 12 A 288 GLN GLU ILE TYR ILE VAL CYS SER GLY GLU MET MET ALA SEQRES 13 A 288 MET TYR ALA ALA ASN ASN ILE SER LYS GLY ILE VAL LYS SEQRES 14 A 288 TYR ALA ASN SER GLY SER VAL ARG LEU GLY GLY LEU ILE SEQRES 15 A 288 CYS ASN SER ARG ASN THR ASP ARG GLU ASP GLU LEU ILE SEQRES 16 A 288 ILE ALA LEU ALA ASN LYS LEU GLY THR GLN MET ILE HIS SEQRES 17 A 288 PHE VAL PRO ARG ASP ASN VAL VAL GLN ARG ALA GLU ILE SEQRES 18 A 288 ARG ARG MET THR VAL ILE GLU TYR ASP PRO LYS ALA LYS SEQRES 19 A 288 GLN ALA ASP GLU TYR ARG ALA LEU ALA ARG LYS VAL VAL SEQRES 20 A 288 ASP ASN LYS LEU LEU VAL ILE PRO ASN PRO ILE THR MET SEQRES 21 A 288 ASP GLU LEU GLU GLU LEU LEU MET GLU PHE GLY ILE MET SEQRES 22 A 288 GLU VAL GLU ASP GLU SER ILE VAL GLY LYS THR ALA GLU SEQRES 23 A 288 GLU VAL HET FES A 290 2 HET FES A 291 2 HET MG A 293 1 HET ATP A5292 31 HETNAM FES FE2/S2 (INORGANIC) CLUSTER HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 2 FES 2(FE2 S2) FORMUL 4 MG MG 2+ FORMUL 5 ATP C10 H16 N5 O13 P3 FORMUL 6 HOH *99(H2 O) HELIX 1 1 GLY A 14 MET A 29 1 16 HELIX 2 2 THR A 45 HIS A 50 1 6 HELIX 3 3 THR A 56 MET A 60 5 5 HELIX 4 4 GLU A 71 VAL A 75 5 5 HELIX 5 5 TYR A 80 GLY A 82 5 3 HELIX 6 6 GLY A 99 GLY A 113 1 15 HELIX 7 7 GLU A 154 LYS A 170 1 17 HELIX 8 8 ARG A 191 GLY A 204 1 14 HELIX 9 9 ASN A 215 ARG A 223 1 9 HELIX 10 10 THR A 226 ASP A 231 1 6 HELIX 11 11 GLN A 236 ASN A 250 1 15 HELIX 12 12 THR A 260 PHE A 271 1 12 SHEET 1 AA 8 LYS A 77 ALA A 78 0 SHEET 2 AA 8 LYS A 84 GLU A 87 -1 O CYS A 85 N LYS A 77 SHEET 3 AA 8 VAL A 33 GLY A 37 1 O VAL A 33 N LYS A 84 SHEET 4 AA 8 PHE A 121 ASP A 125 1 O PHE A 121 N MET A 34 SHEET 5 AA 8 ARG A 3 GLY A 9 1 O ARG A 3 N VAL A 122 SHEET 6 AA 8 GLU A 146 CYS A 151 1 O GLU A 146 N ALA A 6 SHEET 7 AA 8 ARG A 178 ASN A 185 1 O ARG A 178 N ILE A 147 SHEET 8 AA 8 HIS A 209 VAL A 211 1 O HIS A 209 N CYS A 184 LINK OG SER A 16 MG MG A 293 1555 1555 2.28 LINK SG CYS A 97 FE1 FES A 290 1555 1555 2.35 LINK SG CYS A 132 FE1 FES A 291 1555 1555 2.37 LINK MG MG A 293 O HOH A2004 1555 1555 2.34 LINK MG MG A 293 O HOH A2014 1555 1555 2.40 LINK MG MG A 293 O HOH A2099 1555 1555 2.39 LINK MG MG A 293 O1B ATP A5292 1555 1555 2.25 LINK MG MG A 293 O3G ATP A5292 1555 1555 2.39 SITE 1 AC1 5 SER A 16 HOH A2004 HOH A2014 HOH A2099 SITE 2 AC1 5 ATP A5292 SITE 1 AC2 2 CYS A 97 FES A 291 SITE 1 AC3 3 CYS A 132 FES A 290 HOH A2036 SITE 1 AC4 24 LYS A 10 GLY A 11 GLY A 12 ILE A 13 SITE 2 AC4 24 GLY A 14 LYS A 15 SER A 16 THR A 17 SITE 3 AC4 24 ASP A 39 LYS A 41 ASN A 185 PRO A 212 SITE 4 AC4 24 ARG A 213 ASP A 214 VAL A 217 GLN A 218 SITE 5 AC4 24 GLU A 221 GLN A 236 TYR A 240 MG A 293 SITE 6 AC4 24 HOH A2004 HOH A2082 HOH A2097 HOH A2099 CRYST1 70.900 133.300 61.500 90.00 90.00 90.00 C 2 2 21 8 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 0.014104 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016260 0.00000