HEADER OXIDOREDUCTASE 14-OCT-11 3U7R TITLE FERB - FLAVOENZYME NAD(P)H:(ACCEPTOR) OXIDOREDUCTASE (FERB) FROM TITLE 2 PARACOCCUS DENITRIFICANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADPH-DEPENDENT FMN REDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARACOCCUS DENITRIFICANS; SOURCE 3 ORGANISM_TAXID: 318586; SOURCE 4 STRAIN: PD1222; SOURCE 5 GENE: FERB, PDEN_4071; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS ALPHA/BETA TWISTED OPEN-SHEET, LAVOPROTEIN, QUINONE REDUCTASE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.MAREK,T.KLUMPLER,V.SEDLACEK,I.KUCERA REVDAT 3 08-NOV-17 3U7R 1 REMARK REVDAT 2 21-MAY-14 3U7R 1 JRNL REMARK REVDAT 1 24-OCT-12 3U7R 0 JRNL AUTH V.SEDLACEK,T.KLUMPLER,J.MAREK,I.KUCERA JRNL TITL THE STRUCTURAL AND FUNCTIONAL BASIS OF CATALYSIS MEDIATED BY JRNL TITL 2 NAD(P)H:ACCEPTOR OXIDOREDUCTASE (FERB) OF PARACOCCUS JRNL TITL 3 DENITRIFICANS. JRNL REF PLOS ONE V. 9 96262 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 24817153 JRNL DOI 10.1371/JOURNAL.PONE.0096262 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 72133 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3037 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4622 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE SET COUNT : 217 REMARK 3 BIN FREE R VALUE : 0.2240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2848 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 451 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.08000 REMARK 3 B12 (A**2) : 0.00000 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): 0.056 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.054 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.598 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3071 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2969 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4165 ; 1.765 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6859 ; 2.386 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 364 ;13.186 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 135 ;37.940 ;23.926 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 491 ;13.676 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;20.818 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 446 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3362 ; 0.017 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 684 ; 0.004 ; 0.020 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): 1799 ; 1.298 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2892 ; 2.084 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1233 ; 3.648 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1221 ; 5.240 ; 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 2 183 B 2 183 11446 0.08 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 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 2 A 182 REMARK 3 ORIGIN FOR THE GROUP (A): 18.0730 -12.6130 46.0260 REMARK 3 T TENSOR REMARK 3 T11: 0.0097 T22: 0.0277 REMARK 3 T33: 0.0178 T12: -0.0109 REMARK 3 T13: -0.0038 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.1327 L22: 0.3205 REMARK 3 L33: 0.4528 L12: -0.0319 REMARK 3 L13: -0.0351 L23: 0.1293 REMARK 3 S TENSOR REMARK 3 S11: -0.0083 S12: 0.0230 S13: -0.0144 REMARK 3 S21: -0.0149 S22: 0.0104 S23: 0.0349 REMARK 3 S31: 0.0485 S32: -0.0266 S33: -0.0020 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 : B 2 B 182 REMARK 3 ORIGIN FOR THE GROUP (A): 17.3690 11.7430 60.8720 REMARK 3 T TENSOR REMARK 3 T11: 0.0090 T22: 0.0277 REMARK 3 T33: 0.0165 T12: 0.0119 REMARK 3 T13: 0.0056 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.0801 L22: 0.3796 REMARK 3 L33: 0.4502 L12: 0.0020 REMARK 3 L13: -0.0118 L23: 0.1306 REMARK 3 S TENSOR REMARK 3 S11: -0.0041 S12: -0.0144 S13: 0.0078 REMARK 3 S21: 0.0239 S22: 0.0109 S23: 0.0335 REMARK 3 S31: -0.0362 S32: -0.0277 S33: -0.0069 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3U7R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068412. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97522, 0.97714, 0.97753 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111), REMARK 200 HORIZONTALLY FOCUSSING REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75170 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 19.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 76.9 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) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.0 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: AUTO-RICKSHAW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 4000, 0.2M AMMONIUM SULPHATE, REMARK 280 0.1M SODIUM ACETATE, 0.1M MES BUFFER PH 5.00, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 30.51500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.57000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.51500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.57000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: DIMER-TETRAMER EQUILIBRIUM 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: 4130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 61.03000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MSE A 1 REMARK 465 GLU A 184 REMARK 465 HIS A 185 REMARK 465 HIS A 186 REMARK 465 HIS A 187 REMARK 465 HIS A 188 REMARK 465 HIS A 189 REMARK 465 HIS A 190 REMARK 465 MSE B 1 REMARK 465 GLU B 184 REMARK 465 HIS B 185 REMARK 465 HIS B 186 REMARK 465 HIS B 187 REMARK 465 HIS B 188 REMARK 465 HIS B 189 REMARK 465 HIS B 190 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 HOH A 301 O HOH B 469 1.10 REMARK 500 O HOH A 469 O HOH B 327 1.12 REMARK 500 O HOH A 367 O HOH A 499 1.23 REMARK 500 O HOH A 376 O HOH A 512 1.24 REMARK 500 O HOH A 351 O HOH A 464 1.39 REMARK 500 O HOH B 351 O HOH B 462 1.41 REMARK 500 O HOH B 335 O HOH B 515 1.43 REMARK 500 O HOH B 365 O HOH B 472 1.46 REMARK 500 O HOH B 301 O HOH B 477 1.47 REMARK 500 O HOH A 462 O HOH A 467 1.55 REMARK 500 O HOH B 442 O HOH B 499 1.59 REMARK 500 O HOH A 430 O HOH A 483 1.61 REMARK 500 O HOH B 424 O HOH B 480 1.64 REMARK 500 O HOH A 372 O HOH A 473 1.66 REMARK 500 O HOH B 350 O HOH B 515 1.69 REMARK 500 O HOH A 463 O HOH A 467 1.76 REMARK 500 O HOH A 376 O HOH A 517 1.80 REMARK 500 O HOH B 301 O HOH B 478 1.81 REMARK 500 O HOH B 424 O HOH B 476 1.88 REMARK 500 O HOH A 506 O HOH B 463 1.98 REMARK 500 O HOH A 485 O HOH A 494 1.98 REMARK 500 O HOH A 489 O HOH A 521 1.99 REMARK 500 O HOH A 301 O HOH A 458 2.00 REMARK 500 O HOH A 301 O HOH B 327 2.01 REMARK 500 O HOH A 458 O HOH B 327 2.05 REMARK 500 O HOH A 510 O HOH B 519 2.06 REMARK 500 NH2 ARG B 125 O HOH B 348 2.07 REMARK 500 O HOH B 474 O HOH B 501 2.08 REMARK 500 NH2 ARG A 125 O HOH A 368 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 517 O HOH B 358 2655 1.16 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 MSE A 22 CG - SE - CE ANGL. DEV. = -15.1 DEGREES REMARK 500 ARG A 32 CD - NE - CZ ANGL. DEV. = 16.4 DEGREES REMARK 500 ARG A 32 CD - NE - CZ ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG A 32 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 125 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 MSE A 140 CG - SE - CE ANGL. DEV. = -18.9 DEGREES REMARK 500 MSE A 140 CG - SE - CE ANGL. DEV. = -19.5 DEGREES REMARK 500 ARG B 32 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG B 125 NE - CZ - NH1 ANGL. DEV. = 4.5 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 B 53 80.98 -151.19 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 ARG A 32 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FNR A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2PE A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FNR B 201 DBREF 3U7R A 1 182 UNP A1B9E3 A1B9E3_PARDP 1 182 DBREF 3U7R B 1 182 UNP A1B9E3 A1B9E3_PARDP 1 182 SEQADV 3U7R LEU A 183 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R GLU A 184 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R HIS A 185 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R HIS A 186 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R HIS A 187 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R HIS A 188 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R HIS A 189 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R HIS A 190 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R LEU B 183 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R GLU B 184 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R HIS B 185 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R HIS B 186 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R HIS B 187 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R HIS B 188 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R HIS B 189 UNP A1B9E3 EXPRESSION TAG SEQADV 3U7R HIS B 190 UNP A1B9E3 EXPRESSION TAG SEQRES 1 A 190 MSE VAL LYS THR VAL ALA VAL MSE VAL GLY SER LEU ARG SEQRES 2 A 190 LYS ASP SER LEU ASN HIS LYS LEU MSE LYS VAL LEU GLN SEQRES 3 A 190 LYS LEU ALA GLU GLY ARG LEU GLU PHE HIS LEU LEU HIS SEQRES 4 A 190 ILE GLY ASP LEU PRO HIS TYR ASN ASP ASP LEU TRP ALA SEQRES 5 A 190 ASP ALA PRO GLU SER VAL LEU ARG LEU LYS ASP ARG ILE SEQRES 6 A 190 GLU HIS SER ASP ALA VAL LEU ALA ILE THR PRO GLU TYR SEQRES 7 A 190 ASN ARG SER TYR PRO GLY MSE ILE LYS ASN ALA ILE ASP SEQRES 8 A 190 TRP ALA THR ARG PRO TYR GLY GLN ASN SER TRP LYS GLY SEQRES 9 A 190 LYS PRO ALA ALA VAL ILE GLY THR SER PRO GLY VAL ILE SEQRES 10 A 190 GLY ALA ALA LEU ALA GLN ALA ARG LEU LYS ASN ASP LEU SEQRES 11 A 190 LEU HIS VAL GLY THR VAL MSE MSE SER MSE PRO GLU ALA SEQRES 12 A 190 TYR ILE GLN TRP HIS ALA GLU ALA TYR ALA ALA ASP GLY SEQRES 13 A 190 SER VAL THR ASP GLU LYS THR ALA LYS PHE LEU GLN GLY SEQRES 14 A 190 PHE VAL ASP ALA PHE VAL ASP TRP ILE GLU LYS HIS GLY SEQRES 15 A 190 LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 190 MSE VAL LYS THR VAL ALA VAL MSE VAL GLY SER LEU ARG SEQRES 2 B 190 LYS ASP SER LEU ASN HIS LYS LEU MSE LYS VAL LEU GLN SEQRES 3 B 190 LYS LEU ALA GLU GLY ARG LEU GLU PHE HIS LEU LEU HIS SEQRES 4 B 190 ILE GLY ASP LEU PRO HIS TYR ASN ASP ASP LEU TRP ALA SEQRES 5 B 190 ASP ALA PRO GLU SER VAL LEU ARG LEU LYS ASP ARG ILE SEQRES 6 B 190 GLU HIS SER ASP ALA VAL LEU ALA ILE THR PRO GLU TYR SEQRES 7 B 190 ASN ARG SER TYR PRO GLY MSE ILE LYS ASN ALA ILE ASP SEQRES 8 B 190 TRP ALA THR ARG PRO TYR GLY GLN ASN SER TRP LYS GLY SEQRES 9 B 190 LYS PRO ALA ALA VAL ILE GLY THR SER PRO GLY VAL ILE SEQRES 10 B 190 GLY ALA ALA LEU ALA GLN ALA ARG LEU LYS ASN ASP LEU SEQRES 11 B 190 LEU HIS VAL GLY THR VAL MSE MSE SER MSE PRO GLU ALA SEQRES 12 B 190 TYR ILE GLN TRP HIS ALA GLU ALA TYR ALA ALA ASP GLY SEQRES 13 B 190 SER VAL THR ASP GLU LYS THR ALA LYS PHE LEU GLN GLY SEQRES 14 B 190 PHE VAL ASP ALA PHE VAL ASP TRP ILE GLU LYS HIS GLY SEQRES 15 B 190 LEU GLU HIS HIS HIS HIS HIS HIS MODRES 3U7R MSE A 8 MET SELENOMETHIONINE MODRES 3U7R MSE A 22 MET SELENOMETHIONINE MODRES 3U7R MSE A 85 MET SELENOMETHIONINE MODRES 3U7R MSE A 137 MET SELENOMETHIONINE MODRES 3U7R MSE A 138 MET SELENOMETHIONINE MODRES 3U7R MSE A 140 MET SELENOMETHIONINE MODRES 3U7R MSE B 8 MET SELENOMETHIONINE MODRES 3U7R MSE B 22 MET SELENOMETHIONINE MODRES 3U7R MSE B 85 MET SELENOMETHIONINE MODRES 3U7R MSE B 137 MET SELENOMETHIONINE MODRES 3U7R MSE B 138 MET SELENOMETHIONINE MODRES 3U7R MSE B 140 MET SELENOMETHIONINE HET MSE A 8 8 HET MSE A 22 10 HET MSE A 85 8 HET MSE A 137 8 HET MSE A 138 8 HET MSE A 140 9 HET MSE B 8 8 HET MSE B 22 8 HET MSE B 85 8 HET MSE B 137 8 HET MSE B 138 8 HET MSE B 140 8 HET FNR A 201 31 HET 2PE A 202 28 HET FNR B 201 31 HETNAM MSE SELENOMETHIONINE HETNAM FNR 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H- HETNAM 2 FNR BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D- HETNAM 3 FNR RIBITOL HETNAM 2PE NONAETHYLENE GLYCOL HETSYN FNR TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 3 FNR 2(C17 H23 N4 O9 P) FORMUL 4 2PE C18 H38 O10 FORMUL 6 HOH *451(H2 O) HELIX 1 1 SER A 16 GLU A 30 1 15 HELIX 2 2 HIS A 39 LEU A 43 5 5 HELIX 3 3 ASN A 47 ALA A 54 5 8 HELIX 4 4 PRO A 55 HIS A 67 1 13 HELIX 5 5 PRO A 83 ARG A 95 1 13 HELIX 6 6 ALA A 119 HIS A 132 1 14 HELIX 7 7 HIS A 148 TYR A 152 5 5 HELIX 8 8 ASP A 160 GLY A 182 1 23 HELIX 9 9 SER B 16 GLU B 30 1 15 HELIX 10 10 HIS B 39 LEU B 43 5 5 HELIX 11 11 ASN B 47 ALA B 54 5 8 HELIX 12 12 PRO B 55 HIS B 67 1 13 HELIX 13 13 PRO B 83 ARG B 95 1 13 HELIX 14 14 ALA B 119 HIS B 132 1 14 HELIX 15 15 HIS B 148 TYR B 152 5 5 HELIX 16 16 ASP B 160 GLY B 182 1 23 SHEET 1 A 5 LEU A 33 LEU A 37 0 SHEET 2 A 5 LYS A 3 VAL A 9 1 N VAL A 5 O GLU A 34 SHEET 3 A 5 ALA A 70 ILE A 74 1 O ILE A 74 N MSE A 8 SHEET 4 A 5 PRO A 106 SER A 113 1 O PRO A 106 N VAL A 71 SHEET 5 A 5 VAL A 136 MSE A 137 1 O VAL A 136 N ALA A 107 SHEET 1 B 5 LEU A 33 LEU A 37 0 SHEET 2 B 5 LYS A 3 VAL A 9 1 N VAL A 5 O GLU A 34 SHEET 3 B 5 ALA A 70 ILE A 74 1 O ILE A 74 N MSE A 8 SHEET 4 B 5 PRO A 106 SER A 113 1 O PRO A 106 N VAL A 71 SHEET 5 B 5 TYR A 144 GLN A 146 1 O ILE A 145 N SER A 113 SHEET 1 C 5 LEU B 33 LEU B 37 0 SHEET 2 C 5 LYS B 3 VAL B 9 1 N VAL B 5 O HIS B 36 SHEET 3 C 5 ALA B 70 ILE B 74 1 O ILE B 74 N MSE B 8 SHEET 4 C 5 PRO B 106 SER B 113 1 O ALA B 108 N ALA B 73 SHEET 5 C 5 VAL B 136 MSE B 137 1 O VAL B 136 N ALA B 107 SHEET 1 D 5 LEU B 33 LEU B 37 0 SHEET 2 D 5 LYS B 3 VAL B 9 1 N VAL B 5 O HIS B 36 SHEET 3 D 5 ALA B 70 ILE B 74 1 O ILE B 74 N MSE B 8 SHEET 4 D 5 PRO B 106 SER B 113 1 O ALA B 108 N ALA B 73 SHEET 5 D 5 TYR B 144 GLN B 146 1 O ILE B 145 N SER B 113 LINK C VAL A 7 N MSE A 8 1555 1555 1.34 LINK C MSE A 8 N VAL A 9 1555 1555 1.33 LINK C LEU A 21 N MSE A 22 1555 1555 1.32 LINK C MSE A 22 N LYS A 23 1555 1555 1.31 LINK C GLY A 84 N MSE A 85 1555 1555 1.34 LINK C MSE A 85 N ILE A 86 1555 1555 1.34 LINK C VAL A 136 N MSE A 137 1555 1555 1.32 LINK C MSE A 137 N MSE A 138 1555 1555 1.34 LINK C MSE A 138 N SER A 139 1555 1555 1.33 LINK C SER A 139 N MSE A 140 1555 1555 1.33 LINK C MSE A 140 N PRO A 141 1555 1555 1.31 LINK C VAL B 7 N MSE B 8 1555 1555 1.32 LINK C MSE B 8 N VAL B 9 1555 1555 1.31 LINK C LEU B 21 N MSE B 22 1555 1555 1.33 LINK C MSE B 22 N LYS B 23 1555 1555 1.32 LINK C GLY B 84 N MSE B 85 1555 1555 1.34 LINK C MSE B 85 N ILE B 86 1555 1555 1.34 LINK C VAL B 136 N MSE B 137 1555 1555 1.32 LINK C MSE B 137 N MSE B 138 1555 1555 1.34 LINK C MSE B 138 N SER B 139 1555 1555 1.32 LINK C SER B 139 N MSE B 140 1555 1555 1.34 LINK C MSE B 140 N PRO B 141 1555 1555 1.32 CISPEP 1 ARG A 95 PRO A 96 0 -5.73 CISPEP 2 MSE A 140 PRO A 141 0 -25.83 CISPEP 3 ARG B 95 PRO B 96 0 -1.09 CISPEP 4 MSE B 140 PRO B 141 0 24.52 SITE 1 AC1 22 SER A 11 ARG A 13 SER A 16 LEU A 17 SITE 2 AC1 22 ASN A 18 PRO A 76 GLU A 77 TYR A 78 SITE 3 AC1 22 ASN A 79 ARG A 80 SER A 113 PRO A 114 SITE 4 AC1 22 HOH A 305 HOH A 307 HOH A 314 HOH A 321 SITE 5 AC1 22 HOH A 329 HOH A 379 HOH A 396 TYR B 46 SITE 6 AC1 22 THR B 94 ARG B 95 SITE 1 AC2 13 ASP A 42 LEU A 43 PRO A 44 HIS A 45 SITE 2 AC2 13 LEU A 50 HOH A 429 HOH A 501 HOH A 524 SITE 3 AC2 13 GLY B 41 ASP B 42 LEU B 43 HIS B 45 SITE 4 AC2 13 HOH B 463 SITE 1 AC3 22 TYR A 46 ASP A 48 ARG A 95 SER B 11 SITE 2 AC3 22 ARG B 13 SER B 16 LEU B 17 ASN B 18 SITE 3 AC3 22 PRO B 76 GLU B 77 TYR B 78 ASN B 79 SITE 4 AC3 22 ARG B 80 SER B 113 PRO B 114 HOH B 305 SITE 5 AC3 22 HOH B 316 HOH B 320 HOH B 330 HOH B 331 SITE 6 AC3 22 HOH B 333 HOH B 396 CRYST1 61.030 89.140 71.280 90.00 90.00 90.00 P 21 21 2 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 0.016385 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011218 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014029 0.00000