HEADER OXIDOREDUCTASE 08-APR-08 3CRZ TITLE FERREDOXIN-NADP REDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERREDOXIN--NADP+ REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: FPR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS FAD-BINDING FR-TYPE DOMAIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.HAN,E.SCHONBRUNN REVDAT 4 30-AUG-23 3CRZ 1 REMARK REVDAT 3 24-FEB-09 3CRZ 1 VERSN REVDAT 2 04-NOV-08 3CRZ 1 HEADER KEYWDS REVDAT 1 21-OCT-08 3CRZ 0 JRNL AUTH A.WANG,J.C.RODRIGUEZ,H.HAN,E.SCHONBRUNN,M.RIVERA JRNL TITL X-RAY CRYSTALLOGRAPHIC AND SOLUTION STATE NUCLEAR MAGNETIC JRNL TITL 2 RESONANCE SPECTROSCOPIC INVESTIGATIONS OF NADP+ BINDING TO JRNL TITL 3 FERREDOXIN NADP REDUCTASE FROM PSEUDOMONAS AERUGINOSA JRNL REF BIOCHEMISTRY V. 47 8080 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18605699 JRNL DOI 10.1021/BI8007356 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 20651 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) : 0.181 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1446 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 : 2071 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 101 REMARK 3 SOLVENT ATOMS : 288 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.69600 REMARK 3 B22 (A**2) : -0.06400 REMARK 3 B33 (A**2) : -2.63300 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 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.700 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) : 1.180 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.697 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.963 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.683 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 40.90 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : FAD2.PAR REMARK 3 PARAMETER FILE 4 : NAP.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3CRZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047140. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20651 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.610 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.47 REMARK 200 R MERGE FOR SHELL (I) : 0.15700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.440 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 2QDX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM ACETATE, PEG4000, PH 5.6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K 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 33.57000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.74500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.57000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.74500 REMARK 290 SMTRY3 4 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: PISA 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 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 435 O HOH A 537 2.16 REMARK 500 O HOH A 359 O HOH A 403 2.19 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 ASN A 3 47.90 -92.96 REMARK 500 ASN A 16 -165.75 -165.96 REMARK 500 PRO A 72 -56.16 -29.76 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 NAP A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 300 DBREF 3CRZ A 2 258 UNP Q9HYK7 Q9HYK7_PSEAE 2 258 SEQRES 1 A 257 SER ASN LEU TYR THR GLU ARG VAL LEU SER VAL HIS HIS SEQRES 2 A 257 TRP ASN ASP THR LEU PHE SER PHE LYS THR THR ARG ASN SEQRES 3 A 257 PRO GLY LEU ARG PHE LYS THR GLY GLN PHE VAL MET ILE SEQRES 4 A 257 GLY LEU GLU VAL ASP GLY ARG PRO LEU MET ARG ALA TYR SEQRES 5 A 257 SER ILE ALA SER PRO ASN TYR GLU GLU HIS LEU GLU PHE SEQRES 6 A 257 PHE SER ILE LYS VAL PRO ASP GLY PRO LEU THR SER ARG SEQRES 7 A 257 LEU GLN HIS LEU LYS GLU GLY ASP GLU LEU MET VAL SER SEQRES 8 A 257 ARG LYS PRO THR GLY THR LEU VAL HIS ASP ASP LEU LEU SEQRES 9 A 257 PRO GLY LYS HIS LEU TYR LEU LEU SER THR GLY THR GLY SEQRES 10 A 257 MET ALA PRO PHE LEU SER VAL ILE GLN ASP PRO GLU THR SEQRES 11 A 257 TYR GLU ARG TYR GLU LYS VAL ILE LEU VAL HIS GLY VAL SEQRES 12 A 257 ARG TRP VAL SER GLU LEU ALA TYR ALA ASP PHE ILE THR SEQRES 13 A 257 LYS VAL LEU PRO GLU HIS GLU TYR PHE GLY ASP GLN VAL SEQRES 14 A 257 LYS GLU LYS LEU ILE TYR TYR PRO LEU VAL THR ARG GLU SEQRES 15 A 257 PRO PHE ARG ASN GLN GLY ARG GLN THR ASP LEU MET ARG SEQRES 16 A 257 SER GLY LYS LEU PHE GLU ASP ILE GLY LEU PRO PRO MET SEQRES 17 A 257 ASN PRO GLN ASP ASP ARG ALA MET ILE CYS GLY SER PRO SEQRES 18 A 257 SER MET LEU GLU GLU THR SER ALA VAL LEU ASP SER PHE SEQRES 19 A 257 GLY LEU LYS ILE SER PRO ARG MET GLY GLU PRO GLY ASP SEQRES 20 A 257 TYR LEU ILE GLU ARG ALA PHE VAL GLU LYS HET NAP A 305 48 HET FAD A 300 53 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 FAD C27 H33 N9 O15 P2 FORMUL 4 HOH *288(H2 O) HELIX 1 1 LEU A 76 GLN A 81 1 6 HELIX 2 2 VAL A 100 LEU A 104 5 5 HELIX 3 3 MET A 119 ILE A 126 1 8 HELIX 4 4 ASP A 128 TYR A 135 1 8 HELIX 5 5 TRP A 146 LEU A 150 5 5 HELIX 6 6 TYR A 152 LYS A 158 1 7 HELIX 7 7 VAL A 159 HIS A 163 5 5 HELIX 8 8 PHE A 166 LYS A 173 1 8 HELIX 9 9 ARG A 190 GLY A 198 1 9 HELIX 10 10 GLY A 198 GLY A 205 1 8 HELIX 11 11 SER A 221 PHE A 235 1 15 SHEET 1 A 6 ARG A 47 SER A 54 0 SHEET 2 A 6 PHE A 37 VAL A 44 -1 N VAL A 44 O ARG A 47 SHEET 3 A 6 GLU A 88 VAL A 91 -1 O MET A 90 N GLY A 41 SHEET 4 A 6 TYR A 5 ASN A 16 -1 N TYR A 5 O VAL A 91 SHEET 5 A 6 LEU A 19 THR A 25 -1 O LYS A 23 N LEU A 10 SHEET 6 A 6 HIS A 63 ILE A 69 -1 O SER A 68 N PHE A 20 SHEET 1 B 5 LEU A 174 VAL A 180 0 SHEET 2 B 5 LYS A 137 VAL A 144 1 N LEU A 140 O TYR A 177 SHEET 3 B 5 HIS A 109 THR A 115 1 N LEU A 112 O ILE A 139 SHEET 4 B 5 ASP A 214 GLY A 220 1 O CYS A 219 N LEU A 113 SHEET 5 B 5 TYR A 249 ARG A 253 1 O LEU A 250 N ILE A 218 SITE 1 AC1 26 THR A 115 GLY A 143 ARG A 145 THR A 181 SITE 2 AC1 26 ARG A 182 ARG A 190 THR A 192 SER A 221 SITE 3 AC1 26 PRO A 222 SER A 223 MET A 224 GLU A 227 SITE 4 AC1 26 GLU A 257 HOH A 317 HOH A 338 HOH A 352 SITE 5 AC1 26 HOH A 363 HOH A 398 HOH A 454 HOH A 473 SITE 6 AC1 26 HOH A 474 HOH A 475 HOH A 481 HOH A 500 SITE 7 AC1 26 HOH A 504 HOH A 577 SITE 1 AC2 30 PHE A 37 ARG A 51 ALA A 52 TYR A 53 SITE 2 AC2 30 SER A 54 PHE A 67 SER A 68 ILE A 69 SITE 3 AC2 30 GLY A 74 PRO A 75 LEU A 76 THR A 77 SITE 4 AC2 30 THR A 117 ALA A 120 GLU A 252 ARG A 253 SITE 5 AC2 30 ALA A 254 PHE A 255 GLU A 257 LYS A 258 SITE 6 AC2 30 HOH A 320 HOH A 322 HOH A 337 HOH A 341 SITE 7 AC2 30 HOH A 352 HOH A 407 HOH A 409 HOH A 476 SITE 8 AC2 30 HOH A 527 HOH A 577 CRYST1 67.140 73.490 51.540 90.00 90.00 90.00 P 21 21 2 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014894 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019402 0.00000