HEADER OXYGEN STORAGE/TRANSPORT 10-MAR-01 1I7P TITLE CRYSTAL STRUCTURE OF RAT B5R IN COMPLEX WITH FAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADH-CYTOCHROME B5 REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SOLUBLE DOMAIN; COMPND 5 EC: 1.6.2.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: DIA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET 23B KEYWDS ELECTRON TRANSPORT, HEMOGLOBINEMIA, ERYTHROCYTE FUNCTION, FAD- KEYWDS 2 BINDING, NADH-BINDING, OXYGEN STORAGE-TRANSPORT COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.C.BEWLEY,C.C.MAROHNIC,M.J.BARBER REVDAT 3 09-AUG-23 1I7P 1 REMARK SEQADV REVDAT 2 24-FEB-09 1I7P 1 VERSN REVDAT 1 12-DEC-01 1I7P 0 JRNL AUTH M.C.BEWLEY,C.C.MAROHNIC,M.J.BARBER JRNL TITL THE STRUCTURE AND BIOCHEMISTRY OF NADH-DEPENDENT CYTOCHROME JRNL TITL 2 B5 REDUCTASE ARE NOW CONSISTENT. JRNL REF BIOCHEMISTRY V. 40 13574 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11695905 JRNL DOI 10.1021/BI0106336 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 23306 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) : 0.215 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 971 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 : 2183 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 148 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.40 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.800 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1I7P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-01. REMARK 100 THE DEPOSITION ID IS D_1000013008. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : 99 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS - B4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26290 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 11.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.21600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: PROTEIN ATOMS OF 1NDH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, MPD, SODIUM HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 34.04150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.49300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.33300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.49300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.04150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.33300 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 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 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 27 REMARK 465 HIS A 28 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 116 -32.18 -131.88 REMARK 500 TYR A 247 -154.10 -108.39 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 FAD A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NDH RELATED DB: PDB REMARK 900 STRUCTURE OF CYTOCHROME B5 REDUCTASE FROM PIG. REMARK 900 RELATED ID: 1IB0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAT B5R IN COMPLEX WITH FAD AND NAD DBREF 1I7P A 33 300 UNP P20070 NCB5R_RAT 33 300 SEQADV 1I7P MET A 27 UNP P20070 EXPRESSION TAG SEQADV 1I7P HIS A 28 UNP P20070 EXPRESSION TAG SEQADV 1I7P HIS A 29 UNP P20070 EXPRESSION TAG SEQADV 1I7P HIS A 30 UNP P20070 EXPRESSION TAG SEQADV 1I7P HIS A 31 UNP P20070 EXPRESSION TAG SEQADV 1I7P MET A 32 UNP P20070 EXPRESSION TAG SEQADV 1I7P LEU A 52 UNP P20070 ILE 52 CONFLICT SEQADV 1I7P GLU A 115 UNP P20070 ASP 115 CONFLICT SEQRES 1 A 274 MET HIS HIS HIS HIS MET ILE THR LEU GLU ASN PRO ASP SEQRES 2 A 274 ILE LYS TYR PRO LEU ARG LEU ILE ASP LYS GLU ILE LEU SEQRES 3 A 274 SER HIS ASP THR ARG ARG PHE ARG PHE ALA LEU PRO SER SEQRES 4 A 274 PRO GLN HIS ILE LEU GLY LEU PRO ILE GLY GLN HIS ILE SEQRES 5 A 274 TYR LEU SER THR ARG ILE ASP GLY ASN LEU VAL ILE ARG SEQRES 6 A 274 PRO TYR THR PRO VAL SER SER ASP ASP ASP LYS GLY PHE SEQRES 7 A 274 VAL ASP LEU VAL VAL LYS VAL TYR PHE LYS GLU THR HIS SEQRES 8 A 274 PRO LYS PHE PRO ALA GLY GLY LYS MET SER GLN TYR LEU SEQRES 9 A 274 GLU ASN MET ASN ILE GLY ASP THR ILE GLU PHE ARG GLY SEQRES 10 A 274 PRO ASN GLY LEU LEU VAL TYR GLN GLY LYS GLY LYS PHE SEQRES 11 A 274 ALA ILE ARG ALA ASP LYS LYS SER ASN PRO VAL VAL ARG SEQRES 12 A 274 THR VAL LYS SER VAL GLY MET ILE ALA GLY GLY THR GLY SEQRES 13 A 274 ILE THR PRO MET LEU GLN VAL ILE ARG ALA VAL LEU LYS SEQRES 14 A 274 ASP PRO ASN ASP HIS THR VAL CYS TYR LEU LEU PHE ALA SEQRES 15 A 274 ASN GLN SER GLU LYS ASP ILE LEU LEU ARG PRO GLU LEU SEQRES 16 A 274 GLU GLU LEU ARG ASN GLU HIS SER SER ARG PHE LYS LEU SEQRES 17 A 274 TRP TYR THR VAL ASP LYS ALA PRO ASP ALA TRP ASP TYR SEQRES 18 A 274 SER GLN GLY PHE VAL ASN GLU GLU MET ILE ARG ASP HIS SEQRES 19 A 274 LEU PRO PRO PRO GLY GLU GLU THR LEU ILE LEU MET CYS SEQRES 20 A 274 GLY PRO PRO PRO MET ILE GLN PHE ALA CYS LEU PRO ASN SEQRES 21 A 274 LEU GLU ARG VAL GLY HIS PRO LYS GLU ARG CYS PHE THR SEQRES 22 A 274 PHE HET FAD A 301 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 HOH *148(H2 O) HELIX 1 1 GLY A 124 ASN A 132 1 9 HELIX 2 2 GLY A 182 ASP A 196 1 15 HELIX 3 3 LYS A 213 ILE A 215 5 3 HELIX 4 4 LEU A 217 HIS A 228 1 12 HELIX 5 5 ASN A 253 LEU A 261 1 9 HELIX 6 6 PRO A 275 ALA A 282 1 8 HELIX 7 7 CYS A 283 GLY A 291 1 9 HELIX 8 8 PRO A 293 GLU A 295 5 3 SHEET 1 A 6 ASN A 87 TYR A 93 0 SHEET 2 A 6 HIS A 77 ILE A 84 -1 N ILE A 78 O TYR A 93 SHEET 3 A 6 THR A 138 ASN A 145 -1 O GLU A 140 N SER A 81 SHEET 4 A 6 TYR A 42 SER A 53 -1 N TYR A 42 O PHE A 141 SHEET 5 A 6 THR A 56 ALA A 62 -1 O THR A 56 N LEU A 52 SHEET 6 A 6 PHE A 104 LYS A 110 -1 O VAL A 105 N PHE A 61 SHEET 1 B 3 LEU A 148 GLY A 152 0 SHEET 2 B 3 LYS A 155 ILE A 158 -1 O LYS A 155 N GLN A 151 SHEET 3 B 3 VAL A 167 THR A 170 -1 O VAL A 167 N ILE A 158 SHEET 1 C 6 SER A 248 GLN A 249 0 SHEET 2 C 6 PHE A 232 LYS A 240 1 O TYR A 236 N SER A 248 SHEET 3 C 6 VAL A 202 SER A 211 1 O CYS A 203 N LYS A 233 SHEET 4 C 6 SER A 173 GLY A 179 1 O VAL A 174 N TYR A 204 SHEET 5 C 6 THR A 268 CYS A 273 1 O LEU A 269 N GLY A 175 SHEET 6 C 6 CYS A 297 THR A 299 1 N PHE A 298 O ILE A 270 CISPEP 1 GLY A 143 PRO A 144 0 -0.52 SITE 1 AC1 22 ARG A 91 PRO A 92 TYR A 93 THR A 94 SITE 2 AC1 22 VAL A 108 VAL A 109 LYS A 110 TYR A 112 SITE 3 AC1 22 PHE A 113 PHE A 120 GLY A 123 GLY A 124 SITE 4 AC1 22 LYS A 125 MET A 126 SER A 127 THR A 181 SITE 5 AC1 22 THR A 184 PRO A 185 HOH A 337 HOH A 338 SITE 6 AC1 22 HOH A 374 HOH A 417 CRYST1 68.083 70.666 78.986 90.00 90.00 90.00 P 21 21 21 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 0.014688 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014151 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012660 0.00000