HEADER HYDROLASE/TRANSCRIPTION 28-JUL-10 3O5T TITLE STRUCTURE OF DRAG-GLNZ COMPLEX WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DINITROGENASE REDUCTASE ACTIVACTING GLICOHYDROLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.24; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PII-LIKE PROTEIN PZ; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: PZ PROTEIN; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AZOSPIRILLUM BRASILENSE; SOURCE 3 ORGANISM_TAXID: 192; SOURCE 4 STRAIN: FP2; SOURCE 5 GENE: DRAG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PLHPET; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: AZOSPIRILLUM BRASILENSE; SOURCE 13 ORGANISM_TAXID: 192; SOURCE 14 STRAIN: FP2; SOURCE 15 GENE: GLNZ; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PMSA4 KEYWDS ADP BINDING, HYDROLASE-TRANSCRIPTION COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.RAJENDRAN,X.-D.LI,F.K.WINKLER REVDAT 3 01-NOV-23 3O5T 1 REMARK LINK REVDAT 2 13-MAR-13 3O5T 1 JRNL REVDAT 1 05-OCT-11 3O5T 0 JRNL AUTH C.RAJENDRAN,E.C.M.GERHARDT,S.BJELIC,A.GASPERINA, JRNL AUTH 2 M.SCARDUELLI,F.O.PEDROSA,L.S.CHUBATSU,M.MERRICK,E.M.SOUZA, JRNL AUTH 3 F.K.WINKLER,L.F.HUERGO,X.-D.LI JRNL TITL CRYSTAL STRUCTURE OF THE GLNZ-DRAG COMPLEX REVEALS A JRNL TITL 2 DIFFERENT FORM OF PII-TARGET INTERACTION JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 18972 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 22074780 JRNL DOI 10.1073/PNAS.1108038108 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 29470 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1551 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.09 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.14 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2105 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1770 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3027 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 393 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.22000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : 0.34000 REMARK 3 B12 (A**2) : -0.11000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.086 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.164 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3107 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4208 ; 1.843 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 392 ; 5.356 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;35.475 ;23.431 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 524 ;15.896 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;19.141 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 478 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2324 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1945 ; 1.111 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3107 ; 1.953 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1162 ; 3.553 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1101 ; 5.451 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3O5T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060701. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31022 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 70.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.21000 REMARK 200 R SYM FOR SHELL (I) : 0.20500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3MHY AND 3G9D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 8000, 0.2M NACL, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 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 57.82700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.38643 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.20867 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.82700 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.38643 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.20867 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.82700 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.38643 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.20867 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.77287 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 70.41733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.77287 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 70.41733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.77287 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 70.41733 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: HEXAMERIC 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 -57.82700 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 100.15930 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -115.65400 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 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 B 199 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 THR A 2 REMARK 465 GLY B 41 REMARK 465 GLN B 42 REMARK 465 THR B 43 REMARK 465 GLU B 44 REMARK 465 ILE B 45 REMARK 465 TYR B 46 REMARK 465 ARG B 47 REMARK 465 GLY B 48 REMARK 465 ALA B 49 REMARK 465 GLU B 50 REMARK 465 TYR B 51 REMARK 465 SER B 52 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 NH2 ARG A 198 O HOH A 373 2.02 REMARK 500 O HOH B 117 O HOH B 243 2.12 REMARK 500 NH1 ARG A 290 O HOH A 558 2.15 REMARK 500 OE1 GLU B 15 O HOH B 161 2.17 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 82 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 82 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 LEU A 140 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 ARG A 176 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 176 NE - CZ - NH2 ANGL. DEV. = -6.3 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 THR A 59 -153.85 -123.53 REMARK 500 VAL A 94 79.00 65.11 REMARK 500 HIS A 123 36.36 -98.11 REMARK 500 ASN B 108 -125.88 51.14 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 298 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 28 OE2 REMARK 620 2 ASP A 243 OD1 69.7 REMARK 620 3 ASP A 245 OD1 60.7 68.9 REMARK 620 4 ASP A 245 OD2 86.6 121.8 53.3 REMARK 620 5 THR A 246 OG1 158.2 98.7 98.3 84.3 REMARK 620 6 HOH A 565 O 56.2 96.2 116.3 113.5 145.3 REMARK 620 7 HOH A 586 O 123.1 152.2 138.5 85.3 75.8 76.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 299 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 59 OG1 REMARK 620 2 ASP A 60 OD1 90.3 REMARK 620 3 ASP A 61 OD1 88.7 93.4 REMARK 620 4 ASP A 245 OD2 109.1 157.1 75.6 REMARK 620 5 HOH A 345 O 100.2 93.8 168.4 94.4 REMARK 620 N 1 2 3 4 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 298 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 299 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 113 DBREF 3O5T A 1 297 UNP A7XNI2 A7XNI2_AZOBR 1 297 DBREF 3O5T B 1 112 UNP P70731 P70731_AZOBR 1 112 SEQRES 1 A 297 MET THR ASP HIS SER ILE ARG SER ARG ALA LEU GLY ALA SEQRES 2 A 297 TYR LEU GLY LEU ALA CYS GLY ASP ALA LEU GLY ALA THR SEQRES 3 A 297 VAL GLU PHE LEU THR LYS GLY GLU ILE ALA HIS GLN TYR SEQRES 4 A 297 GLY VAL HIS LYS HIS ILE LYS GLY GLY GLY TRP LEU LYS SEQRES 5 A 297 LEU PRO ALA GLY GLN VAL THR ASP ASP THR GLU MET SER SEQRES 6 A 297 ILE HIS LEU GLY ARG ALA ILE LEU ALA ALA PRO GLU TRP SEQRES 7 A 297 ASP ALA ARG ARG ALA ALA GLU GLU PHE ALA VAL TRP LEU SEQRES 8 A 297 LYS GLY VAL PRO VAL ASP VAL GLY ASP THR THR ARG ARG SEQRES 9 A 297 GLY ILE ARG ARG PHE ILE MET HIS GLY THR LEU SER GLU SEQRES 10 A 297 PRO GLU SER GLU TYR HIS ALA GLY ASN GLY ALA ALA MET SEQRES 11 A 297 ARG ASN LEU PRO VAL ALA LEU ALA THR LEU GLY ASP ASP SEQRES 12 A 297 ALA ALA PHE GLU ARG TRP THR VAL GLU GLN ALA HIS ILE SEQRES 13 A 297 THR HIS CYS ASN ALA MET SER ASP ALA ALA THR LEU THR SEQRES 14 A 297 LEU GLY HIS MET VAL ARG ARG LEU VAL LEU GLY GLY ASP SEQRES 15 A 297 VAL ARG ASP VAL ARG ASP GLU SER ASN LYS LEU ILE ALA SEQRES 16 A 297 LYS HIS ARG GLN PHE LYS PHE GLN PRO TYR ARG GLY LEU SEQRES 17 A 297 ALA THR ALA TYR ILE VAL ASP THR MET GLN THR VAL MET SEQRES 18 A 297 HIS TYR TYR PHE GLN THR ASP SER VAL GLU SER CYS VAL SEQRES 19 A 297 VAL GLU THR VAL ASN GLN GLY GLY ASP ALA ASP THR THR SEQRES 20 A 297 GLY ALA ILE ALA GLY MET LEU ALA GLY ALA THR TYR GLY SEQRES 21 A 297 VAL GLU THR ILE PRO PRO ARG TRP LEU ARG LYS LEU ASP SEQRES 22 A 297 ARG ASP VAL TYR ASN GLU ILE CYS ALA GLN VAL ASP GLY SEQRES 23 A 297 LEU LEU ALA ARG ALA PRO ALA LEU LYS GLN GLY SEQRES 1 B 112 MET LYS LEU VAL MET ALA ILE ILE LYS PRO PHE LYS LEU SEQRES 2 B 112 ASP GLU VAL ARG GLU ALA LEU THR SER LEU GLY ILE GLN SEQRES 3 B 112 GLY LEU THR VAL SER GLU VAL LYS GLY PHE GLY ARG GLN SEQRES 4 B 112 LYS GLY GLN THR GLU ILE TYR ARG GLY ALA GLU TYR SER SEQRES 5 B 112 VAL SER PHE LEU PRO LYS VAL LYS VAL GLU VAL ALA VAL SEQRES 6 B 112 SER ASP ASP GLN TYR GLU GLN VAL VAL GLU ALA ILE GLN SEQRES 7 B 112 LYS ALA ALA ASN THR GLY ARG ILE GLY ASP GLY LYS ILE SEQRES 8 B 112 PHE VAL LEU ASP ILE ALA GLN ALA VAL ARG ILE ARG THR SEQRES 9 B 112 GLY GLU THR ASN THR GLU ALA LEU HET MG A 298 1 HET MG A 299 1 HET ADP B 113 27 HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 3 MG 2(MG 2+) FORMUL 5 ADP C10 H15 N5 O10 P2 FORMUL 6 HOH *393(H2 O) HELIX 1 1 ASP A 3 ALA A 25 1 23 HELIX 2 2 THR A 26 GLU A 28 5 3 HELIX 3 3 THR A 31 GLY A 40 1 10 HELIX 4 4 GLY A 48 LYS A 52 5 5 HELIX 5 5 THR A 59 ALA A 74 1 16 HELIX 6 6 ASP A 79 GLY A 93 1 15 HELIX 7 7 GLY A 99 GLY A 113 1 15 HELIX 8 8 ALA A 128 ARG A 131 5 4 HELIX 9 9 ASN A 132 THR A 139 1 8 HELIX 10 10 ASP A 142 HIS A 155 1 14 HELIX 11 11 ASN A 160 LEU A 179 1 20 HELIX 12 12 ASP A 182 HIS A 197 1 16 HELIX 13 13 ARG A 198 LYS A 201 5 4 HELIX 14 14 TYR A 212 THR A 227 1 16 HELIX 15 15 SER A 229 ASN A 239 1 11 HELIX 16 16 ASP A 243 GLY A 260 1 18 HELIX 17 17 VAL A 261 ILE A 264 5 4 HELIX 18 18 PRO A 265 ARG A 270 1 6 HELIX 19 19 ASP A 273 ALA A 289 1 17 HELIX 20 20 ARG A 290 LYS A 295 5 6 HELIX 21 21 LYS B 12 LEU B 23 1 12 HELIX 22 22 GLN B 69 ASN B 82 1 14 HELIX 23 23 THR B 107 LEU B 112 5 6 SHEET 1 A 4 THR B 29 PHE B 36 0 SHEET 2 A 4 PHE B 55 VAL B 65 -1 O LEU B 56 N GLY B 35 SHEET 3 A 4 LYS B 2 ILE B 8 -1 N ALA B 6 O VAL B 61 SHEET 4 A 4 GLY B 89 ASP B 95 -1 O LYS B 90 N ILE B 7 LINK OE2 GLU A 28 MG MG A 298 1555 1555 2.83 LINK OG1 THR A 59 MG MG A 299 1555 1555 2.40 LINK OD1 ASP A 60 MG MG A 299 1555 1555 2.14 LINK OD1 ASP A 61 MG MG A 299 1555 1555 2.46 LINK OD1 ASP A 243 MG MG A 298 1555 1555 2.21 LINK OD1 ASP A 245 MG MG A 298 1555 1555 2.47 LINK OD2 ASP A 245 MG MG A 298 1555 1555 2.49 LINK OD2 ASP A 245 MG MG A 299 1555 1555 2.14 LINK OG1 THR A 246 MG MG A 298 1555 1555 2.47 LINK MG MG A 298 O HOH A 565 1555 1555 2.33 LINK MG MG A 298 O HOH A 586 1555 1555 2.93 LINK MG MG A 299 O HOH A 345 1555 1555 2.28 CISPEP 1 GLN A 203 PRO A 204 0 -0.59 SITE 1 AC1 6 GLU A 28 ASP A 243 ASP A 245 THR A 246 SITE 2 AC1 6 HOH A 565 HOH A 586 SITE 1 AC2 5 THR A 59 ASP A 60 ASP A 61 ASP A 245 SITE 2 AC2 5 HOH A 345 SITE 1 AC3 24 HOH A 482 ILE B 7 GLY B 27 LEU B 28 SITE 2 AC3 24 THR B 29 GLY B 35 PHE B 36 GLY B 37 SITE 3 AC3 24 ARG B 38 GLN B 39 LYS B 58 GLU B 62 SITE 4 AC3 24 VAL B 63 ALA B 64 ILE B 86 GLY B 87 SITE 5 AC3 24 GLY B 89 LYS B 90 ARG B 101 ARG B 103 SITE 6 AC3 24 HOH B 118 HOH B 143 HOH B 236 HOH B 256 CRYST1 115.654 115.654 105.626 90.00 90.00 120.00 H 3 9 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 0.008646 0.004992 0.000000 0.00000 SCALE2 0.000000 0.009984 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009467 0.00000