HEADER OXIDOREDUCTASE 21-JAN-05 2BIH TITLE CRYSTAL STRUCTURE OF THE MOLYBDENUM-CONTAINING NITRATE REDUCING TITLE 2 FRAGMENT OF PICHIA ANGUSTA ASSIMILATORY NITRATE REDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRATE REDUCTASE [NADPH]; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MOCO-BINDING DOMAIN, DIMERIZATION DOMAIN, RESIDUES 11-13, COMPND 5 20-478; COMPND 6 SYNONYM: ASSIMILATORY NITRATE REDUCTASE; COMPND 7 EC: 1.7.1.2; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PICHIA ANGUSTA; SOURCE 3 ORGANISM_TAXID: 4905; SOURCE 4 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: Y-11430; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PPICZB; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: SNAR1-PPICZB KEYWDS FLAVOPROTEIN, NITRATE ASSIMILATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.FISCHER,G.BARBIER,H.-J.HECHT,R.R.MENDEL,W.H.CAMPBELL,G.SCHWARZ REVDAT 5 13-DEC-23 2BIH 1 LINK REVDAT 4 13-JUL-11 2BIH 1 VERSN REVDAT 3 24-FEB-09 2BIH 1 VERSN REVDAT 2 06-APR-05 2BIH 1 JRNL REVDAT 1 30-MAR-05 2BIH 0 JRNL AUTH K.FISCHER,G.BARBIER,H.-J.HECHT,R.R.MENDEL,W.H.CAMPBELL, JRNL AUTH 2 G.SCHWARZ JRNL TITL STRUCTURAL BASIS OF EUKARYOTIC NITRATE REDUCTION: CRYSTAL JRNL TITL 2 STRUCTURES OF THE NITRATE REDUCTASE ACTIVE SITE JRNL REF PLANT CELL V. 17 1167 2005 JRNL REFN ISSN 1040-4651 JRNL PMID 15772287 JRNL DOI 10.1105/TPC.104.029694 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : RESTRAINED TLS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 17366 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 880 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) : 11.46 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 65.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 239 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 9 REMARK 3 BIN FREE R VALUE : 0.4440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3654 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.45400 REMARK 3 B22 (A**2) : 2.45400 REMARK 3 B33 (A**2) : -3.68100 REMARK 3 B12 (A**2) : 1.22700 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): 0.785 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.325 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.223 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.854 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3784 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3366 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5140 ; 1.901 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7829 ; 0.848 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 452 ; 8.406 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 178 ;33.908 ;23.371 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 637 ;16.601 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;17.866 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 529 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4193 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 793 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 817 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3664 ; 0.203 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1846 ; 0.191 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2209 ; 0.092 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 141 ; 0.129 ; 0.200 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): 10 ; 0.300 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 58 ; 0.258 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.535 ; 0.200 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): 2840 ; 0.873 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3654 ; 1.042 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1871 ; 1.650 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1486 ; 2.474 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 274 REMARK 3 ORIGIN FOR THE GROUP (A): 53.0522 -2.6290 111.0992 REMARK 3 T TENSOR REMARK 3 T11: 0.0400 T22: -0.0431 REMARK 3 T33: -0.0530 T12: 0.0641 REMARK 3 T13: -0.0394 T23: -0.0308 REMARK 3 L TENSOR REMARK 3 L11: 0.4800 L22: 0.3876 REMARK 3 L33: 0.6776 L12: -0.0502 REMARK 3 L13: -0.0964 L23: 0.0945 REMARK 3 S TENSOR REMARK 3 S11: 0.0351 S12: 0.0435 S13: -0.0952 REMARK 3 S21: -0.0953 S22: -0.0337 S23: 0.0237 REMARK 3 S31: 0.1522 S32: 0.0917 S33: -0.0014 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 275 A 478 REMARK 3 ORIGIN FOR THE GROUP (A): 37.5478 8.6078 125.1463 REMARK 3 T TENSOR REMARK 3 T11: -0.0298 T22: -0.0386 REMARK 3 T33: -0.0223 T12: 0.0056 REMARK 3 T13: -0.0313 T23: -0.0247 REMARK 3 L TENSOR REMARK 3 L11: 0.6562 L22: 0.3813 REMARK 3 L33: 0.5325 L12: -0.1664 REMARK 3 L13: 0.0236 L23: 0.0693 REMARK 3 S TENSOR REMARK 3 S11: 0.0310 S12: -0.0794 S13: -0.0397 REMARK 3 S21: -0.0686 S22: -0.0332 S23: 0.0951 REMARK 3 S31: 0.0837 S32: -0.0664 S33: 0.0022 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1479 A 1479 REMARK 3 ORIGIN FOR THE GROUP (A): 50.0842 0.3261 108.5658 REMARK 3 T TENSOR REMARK 3 T11: 0.0068 T22: -0.0106 REMARK 3 T33: -0.0159 T12: 0.0532 REMARK 3 T13: -0.0610 T23: -0.0597 REMARK 3 L TENSOR REMARK 3 L11: 3.4992 L22: 1.2726 REMARK 3 L33: 25.9371 L12: 2.1102 REMARK 3 L13: -9.5268 L23: -5.7452 REMARK 3 S TENSOR REMARK 3 S11: -0.2801 S12: -0.0418 S13: 0.0810 REMARK 3 S21: 0.0452 S22: 0.1733 S23: 0.0159 REMARK 3 S31: 0.7560 S32: 0.1773 S33: 0.1067 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2BIH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1290021008. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL 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) : 1.005 REMARK 200 MONOCHROMATOR : SI DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : 17438 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1OGP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 102.02867 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 204.05733 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 153.04300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 255.07167 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 51.01433 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 102.02867 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 204.05733 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 255.07167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 153.04300 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 51.01433 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: 5890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.500000 -0.866025 0.000000 38.37000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 66.45879 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 255.07167 REMARK 400 REMARK 400 COMPOUND REMARK 400 HIS TAG INSERTION OF (HHHHHHD) BETWEEN E13 AND I14 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 GLY A 11 REMARK 465 LEU A 12 REMARK 465 GLU A 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 HIS A 19 REMARK 465 GLN A 20 REMARK 465 ASP A 21 REMARK 465 ILE A 22 REMARK 465 THR A 23 REMARK 465 GLU A 24 REMARK 465 LEU A 25 REMARK 465 ASP A 479 REMARK 465 THR A 480 REMARK 465 GLY A 481 REMARK 465 GLN A 482 REMARK 465 ALA A 483 REMARK 465 GLY A 484 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2049 O HOH A 2049 10665 1.73 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 CYS A 383 CB CYS A 383 SG -0.116 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 216 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 216 NE - CZ - NH2 ANGL. DEV. = -3.2 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 ASP A 47 43.33 -82.54 REMARK 500 HIS A 63 142.62 -174.88 REMARK 500 GLU A 100 56.65 -92.21 REMARK 500 ASN A 101 -31.24 174.76 REMARK 500 ILE A 102 -58.53 -25.87 REMARK 500 ARG A 181 68.77 66.26 REMARK 500 PRO A 197 175.30 -59.64 REMARK 500 THR A 204 -151.05 -158.35 REMARK 500 LYS A 254 -35.48 -131.83 REMARK 500 ASP A 287 107.53 -160.41 REMARK 500 TYR A 299 -92.13 -119.74 REMARK 500 GLU A 411 2.59 -70.00 REMARK 500 ASN A 429 96.98 -60.53 REMARK 500 PRO A 455 -175.57 -69.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE HETGROUP CALLED MTV IN THIS PDB ENTRY IS SIMILAR TO MTQ REMARK 600 EXCEPT FOR THE FACT THAT THE OM2-MO BOND IS A REDUCED SINGLE REMARK 600 BOND HAVING ONE EXTRA HYDROGEN. REMARK 600 REMARK 600 FOR METAL ATOM MOM1 MTV A1479 THE COORDINATION ANGLES ARE: REMARK 600 1 MTV 1479A S1' REMARK 600 2 MTV 1479A S2' 79.7 REMARK 600 3 MTV 1479A OM2 82.6 142.1 REMARK 600 4 MTV 1479A OM1 113.8 107.3 110.5 REMARK 600 1 2 3 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 MTV A1479 MOM1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 139 SG REMARK 620 2 MTV A1479 S1' 143.0 REMARK 620 3 MTV A1479 S2' 87.1 79.7 REMARK 620 4 MTV A1479 OM1 103.1 113.8 107.3 REMARK 620 5 MTV A1479 OM2 87.3 82.6 142.1 110.5 REMARK 620 N 1 2 3 4 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTV A1479 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BII RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NITRATE-REDUCING FRAGMENT OF ASSIMILATORY REMARK 900 NITRATE REDUCTASE FROM PICHIA ANGUSTA REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHORS INDICATE THAT THE CONFLICT DESCRIBED BELOW REMARK 999 IS PROBABLY DUE TO ERROR IN THE SEQUENCE DATABASE REMARK 999 ANNOTATION, SINCE IN THIS STRUCTURE AS WELL IN THE HIGH REMARK 999 RESOLUTION STRUCTURE (PDB ID: 2BII), NO SIDE CHAIN DENSITY REMARK 999 FOR AN ARGININE COULD BE OBSERVED. REMARK 999 REMARK 999 N-TERMINAL SEQUENCING OF THE PROTEIN CRYSTAL CONFIRMS REMARK 999 THAT THE SEQUENCE BEINGS AT RESIDUE 11. RESIDUES REMARK 999 RESIDUES 479-484 ARE NOT VISIBLE IN THE CRYSTAL REMARK 999 STRUCTURE DBREF 2BIH A 21 480 UNP P49050 NIA_PICAN 19 478 SEQADV 2BIH GLY A 11 UNP P49050 EXPRESSION TAG SEQADV 2BIH LEU A 12 UNP P49050 EXPRESSION TAG SEQADV 2BIH GLU A 13 UNP P49050 EXPRESSION TAG SEQADV 2BIH HIS A 14 UNP P49050 EXPRESSION TAG SEQADV 2BIH HIS A 15 UNP P49050 EXPRESSION TAG SEQADV 2BIH HIS A 16 UNP P49050 EXPRESSION TAG SEQADV 2BIH HIS A 17 UNP P49050 EXPRESSION TAG SEQADV 2BIH HIS A 18 UNP P49050 EXPRESSION TAG SEQADV 2BIH HIS A 19 UNP P49050 EXPRESSION TAG SEQADV 2BIH GLN A 20 UNP P49050 EXPRESSION TAG SEQADV 2BIH GLY A 481 UNP P49050 EXPRESSION TAG SEQADV 2BIH GLN A 482 UNP P49050 EXPRESSION TAG SEQADV 2BIH ALA A 483 UNP P49050 EXPRESSION TAG SEQADV 2BIH GLY A 484 UNP P49050 EXPRESSION TAG SEQADV 2BIH GLY A 203 UNP P49050 ARG 201 CONFLICT SEQRES 1 A 474 GLY LEU GLU HIS HIS HIS HIS HIS HIS GLN ASP ILE THR SEQRES 2 A 474 GLU LEU PRO PHE PRO VAL ARG GLN ASP SER PRO LEU THR SEQRES 3 A 474 GLU VAL LEU PRO THR ASP LEU LYS THR LYS ASP ASN PHE SEQRES 4 A 474 VAL ALA ARG ASP PRO ASP LEU LEU ARG LEU THR GLY SER SEQRES 5 A 474 HIS PRO PHE ASN SER GLU PRO PRO LEU THR LYS LEU TYR SEQRES 6 A 474 ASP SER GLY PHE LEU THR PRO VAL SER LEU HIS PHE VAL SEQRES 7 A 474 ARG ASN HIS GLY PRO VAL PRO TYR VAL PRO ASP GLU ASN SEQRES 8 A 474 ILE LEU ASP TRP GLU VAL SER ILE GLU GLY MET VAL GLU SEQRES 9 A 474 THR PRO TYR LYS ILE LYS LEU SER ASP ILE MET GLU GLN SEQRES 10 A 474 PHE ASP ILE TYR SER THR PRO VAL THR MET VAL CYS ALA SEQRES 11 A 474 GLY ASN ARG ARG LYS GLU GLN ASN MET VAL LYS LYS GLY SEQRES 12 A 474 ALA GLY PHE ASN TRP GLY ALA ALA GLY THR SER THR SER SEQRES 13 A 474 LEU TRP THR GLY CYS MET LEU GLY ASP VAL ILE GLY LYS SEQRES 14 A 474 ALA ARG PRO SER LYS ARG ALA ARG PHE VAL TRP MET GLU SEQRES 15 A 474 GLY ALA ASP ASN PRO ALA ASN GLY ALA TYR GLY THR CYS SEQRES 16 A 474 ILE ARG LEU SER TRP CYS MET ASP PRO GLU ARG CYS ILE SEQRES 17 A 474 MET ILE ALA TYR GLN GLN ASN GLY GLU TRP LEU HIS PRO SEQRES 18 A 474 ASP HIS GLY LYS PRO LEU ARG VAL VAL ILE PRO GLY VAL SEQRES 19 A 474 ILE GLY GLY ARG SER VAL LYS TRP LEU LYS LYS LEU VAL SEQRES 20 A 474 VAL SER ASP ARG PRO SER GLU ASN TRP TYR HIS TYR PHE SEQRES 21 A 474 ASP ASN ARG VAL LEU PRO THR MET VAL THR PRO GLU MET SEQRES 22 A 474 ALA LYS SER ASP ASP ARG TRP TRP LYS ASP GLU ARG TYR SEQRES 23 A 474 ALA ILE TYR ASP LEU ASN LEU GLN THR ILE ILE CYS LYS SEQRES 24 A 474 PRO GLU ASN GLN GLN VAL ILE LYS ILE SER GLU ASP GLU SEQRES 25 A 474 TYR GLU ILE ALA GLY PHE GLY TYR ASN GLY GLY GLY VAL SEQRES 26 A 474 ARG ILE GLY ARG ILE GLU VAL SER LEU ASP LYS GLY LYS SEQRES 27 A 474 SER TRP LYS LEU ALA ASP ILE ASP TYR PRO GLU ASP ARG SEQRES 28 A 474 TYR ARG GLU ALA GLY TYR PHE ARG LEU PHE GLY GLY LEU SEQRES 29 A 474 VAL ASN VAL CYS ASP ARG MET SER CYS LEU CYS TRP CYS SEQRES 30 A 474 PHE TRP LYS LEU LYS VAL PRO LEU SER GLU LEU ALA ARG SEQRES 31 A 474 SER LYS ASP ILE LEU ILE ARG GLY MET ASP GLU ARG MET SEQRES 32 A 474 MET VAL GLN PRO ARG THR MET TYR TRP ASN VAL THR SER SEQRES 33 A 474 MET LEU ASN ASN TRP TRP TYR ARG VAL ALA ILE ILE ARG SEQRES 34 A 474 GLU GLY GLU SER LEU ARG PHE GLU HIS PRO VAL VAL ALA SEQRES 35 A 474 ASN LYS PRO GLY GLY TRP MET ASP ARG VAL LYS ALA GLU SEQRES 36 A 474 GLY GLY ASP ILE LEU ASP ASN ASN TRP GLY GLU VAL ASP SEQRES 37 A 474 ASP THR GLY GLN ALA GLY HET MTV A1479 27 HETNAM MTV (MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(IV) FORMUL 2 MTV C10 H9 MO N5 O8 P S2 1- FORMUL 3 HOH *59(H2 O) HELIX 1 1 LEU A 39 LYS A 44 1 6 HELIX 2 2 PRO A 70 SER A 77 1 8 HELIX 3 3 PRO A 82 HIS A 86 5 5 HELIX 4 4 ASN A 101 ASP A 104 5 4 HELIX 5 5 LEU A 121 PHE A 128 1 8 HELIX 6 6 ARG A 143 LYS A 151 1 9 HELIX 7 7 LEU A 173 ALA A 180 1 8 HELIX 8 8 LEU A 208 MET A 212 1 5 HELIX 9 9 HIS A 230 GLY A 234 5 5 HELIX 10 10 GLY A 246 SER A 249 5 4 HELIX 11 11 ASN A 265 ASP A 271 1 7 HELIX 12 12 THR A 280 SER A 286 1 7 HELIX 13 13 ASP A 287 LYS A 292 5 6 HELIX 14 14 ASP A 293 TYR A 296 5 4 HELIX 15 15 PRO A 358 ALA A 365 1 8 HELIX 16 16 ASN A 376 ARG A 380 5 5 HELIX 17 17 LEU A 395 ARG A 400 1 6 HELIX 18 18 GLY A 457 GLY A 466 1 10 SHEET 1 AA 3 LEU A 57 ARG A 58 0 SHEET 2 AA 3 ASN A 66 GLU A 68 -1 O GLU A 68 N LEU A 57 SHEET 3 AA 3 VAL A 88 ARG A 89 -1 O VAL A 88 N SER A 67 SHEET 1 AB 5 TYR A 117 LYS A 120 0 SHEET 2 AB 5 GLU A 106 GLY A 111 -1 O VAL A 107 N ILE A 119 SHEET 3 AB 5 LEU A 253 SER A 259 1 O LYS A 254 N SER A 108 SHEET 4 AB 5 PHE A 188 GLY A 193 -1 O PHE A 188 N SER A 259 SHEET 5 AB 5 GLY A 203 ARG A 207 -1 O THR A 204 N MET A 191 SHEET 1 AC 4 TYR A 131 VAL A 138 0 SHEET 2 AC 4 THR A 163 MET A 172 -1 O SER A 164 N MET A 137 SHEET 3 AC 4 MET A 219 GLN A 224 -1 O ILE A 220 N CYS A 171 SHEET 4 AC 4 ARG A 238 VAL A 240 -1 O ARG A 238 N ALA A 221 SHEET 1 AD 4 TYR A 131 VAL A 138 0 SHEET 2 AD 4 THR A 163 MET A 172 -1 O SER A 164 N MET A 137 SHEET 3 AD 4 MET A 219 GLN A 224 -1 O ILE A 220 N CYS A 171 SHEET 4 AD 4 GLU A 227 TRP A 228 -1 O GLU A 227 N GLN A 224 SHEET 1 AE 4 GLN A 304 LYS A 309 0 SHEET 2 AE 4 GLU A 322 TYR A 330 -1 O ALA A 326 N CYS A 308 SHEET 3 AE 4 CYS A 387 PRO A 394 -1 O CYS A 387 N GLY A 329 SHEET 4 AE 4 ASP A 354 ASP A 356 -1 O ASP A 354 N LYS A 390 SHEET 1 AF 6 VAL A 315 LYS A 317 0 SHEET 2 AF 6 SER A 443 GLU A 447 -1 O LEU A 444 N ILE A 316 SHEET 3 AF 6 TYR A 433 GLU A 440 -1 O ALA A 436 N GLU A 447 SHEET 4 AF 6 ASP A 403 ASP A 410 -1 O ILE A 404 N VAL A 435 SHEET 5 AF 6 ILE A 337 SER A 343 -1 N GLY A 338 O MET A 409 SHEET 6 AF 6 LYS A 351 LEU A 352 -1 O LYS A 351 N VAL A 342 SHEET 1 AG 2 PHE A 368 LEU A 370 0 SHEET 2 AG 2 GLY A 373 VAL A 375 -1 O GLY A 373 N LEU A 370 LINK SG CYS A 139 MOM1 MTV A1479 1555 1555 2.66 CISPEP 1 HIS A 63 PRO A 64 0 -4.48 CISPEP 2 LYS A 235 PRO A 236 0 11.44 CISPEP 3 LYS A 309 PRO A 310 0 -1.15 SITE 1 AC1 21 HIS A 86 PHE A 87 VAL A 88 ARG A 89 SITE 2 AC1 21 HIS A 91 MET A 137 CYS A 139 ALA A 140 SITE 3 AC1 21 ASP A 195 TYR A 202 ASP A 232 HIS A 233 SITE 4 AC1 21 ARG A 238 ILE A 245 GLY A 246 GLY A 247 SITE 5 AC1 21 SER A 249 VAL A 250 LYS A 251 TRP A 252 SITE 6 AC1 21 ASN A 272 CRYST1 76.740 76.740 306.086 90.00 90.00 120.00 P 61 2 2 12 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 0.013031 0.007523 0.000000 0.00000 SCALE2 0.000000 0.015047 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003267 0.00000