HEADER OXIDOREDUCTASE 08-AUG-00 1GCU TITLE CRYSTAL STRUCTURE OF RAT BILIVERDIN REDUCTASE AT 1.4 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: BILIVERDIN REDUCTASE A; COMPND 3 CHAIN: A; COMPND 4 EC: 1.3.1.24; COMPND 5 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BILIVERDIN, ROSSMANN FOLD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KIKUCHI,S.Y.PARK,Y.SHIRO REVDAT 5 27-DEC-23 1GCU 1 REMARK REVDAT 4 11-OCT-17 1GCU 1 REMARK REVDAT 3 24-FEB-09 1GCU 1 VERSN REVDAT 2 28-JAN-03 1GCU 1 REMARK REVDAT 1 08-FEB-01 1GCU 0 JRNL AUTH A.KIKUCHI,S.Y.PARK,H.MIYATAKE,D.SUN,M.SATO,T.YOSHIDA,Y.SHIRO JRNL TITL CRYSTAL STRUCTURE OF RAT BILIVERDIN REDUCTASE. JRNL REF NAT.STRUCT.BIOL. V. 8 221 2001 JRNL REFN ISSN 1072-8368 JRNL PMID 11224565 JRNL DOI 10.1038/84955 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.70 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) (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 71120 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 SET) : 0.219 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3606 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 : 2335 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 294 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.30 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) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.600 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 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 1GCU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-AUG-00. REMARK 100 THE DEPOSITION ID IS D_1000005037. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 379020 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 32.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 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) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.32400 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: NULL REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (NH4)2SO4, NA CITRATE, NA/K TARTRATE, REMARK 280 PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K 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 29.34100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.93300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.24350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.93300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.34100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.24350 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 GLN A 293 REMARK 465 LYS A 294 REMARK 465 LYS A 295 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 GLU A 52 -2.32 73.24 REMARK 500 SER A 234 73.93 -118.88 REMARK 500 REMARK 500 REMARK: NULL DBREF 1GCU A 1 295 UNP P46844 BIEA_RAT 1 295 SEQRES 1 A 295 MET ASP ALA GLU PRO LYS ARG LYS PHE GLY VAL VAL VAL SEQRES 2 A 295 VAL GLY VAL GLY ARG ALA GLY SER VAL ARG LEU ARG ASP SEQRES 3 A 295 LEU LYS ASP PRO ARG SER ALA ALA PHE LEU ASN LEU ILE SEQRES 4 A 295 GLY PHE VAL SER ARG ARG GLU LEU GLY SER LEU ASP GLU SEQRES 5 A 295 VAL ARG GLN ILE SER LEU GLU ASP ALA LEU ARG SER GLN SEQRES 6 A 295 GLU ILE ASP VAL ALA TYR ILE CYS SER GLU SER SER SER SEQRES 7 A 295 HIS GLU ASP TYR ILE ARG GLN PHE LEU GLN ALA GLY LYS SEQRES 8 A 295 HIS VAL LEU VAL GLU TYR PRO MET THR LEU SER PHE ALA SEQRES 9 A 295 ALA ALA GLN GLU LEU TRP GLU LEU ALA ALA GLN LYS GLY SEQRES 10 A 295 ARG VAL LEU HIS GLU GLU HIS VAL GLU LEU LEU MET GLU SEQRES 11 A 295 GLU PHE GLU PHE LEU ARG ARG GLU VAL LEU GLY LYS GLU SEQRES 12 A 295 LEU LEU LYS GLY SER LEU ARG PHE THR ALA SER PRO LEU SEQRES 13 A 295 GLU GLU GLU ARG PHE GLY PHE PRO ALA PHE SER GLY ILE SEQRES 14 A 295 SER ARG LEU THR TRP LEU VAL SER LEU PHE GLY GLU LEU SEQRES 15 A 295 SER LEU ILE SER ALA THR LEU GLU GLU ARG LYS GLU ASP SEQRES 16 A 295 GLN TYR MET LYS MET THR VAL GLN LEU GLU THR GLN ASN SEQRES 17 A 295 LYS GLY LEU LEU SER TRP ILE GLU GLU LYS GLY PRO GLY SEQRES 18 A 295 LEU LYS ARG ASN ARG TYR VAL ASN PHE GLN PHE THR SER SEQRES 19 A 295 GLY SER LEU GLU GLU VAL PRO SER VAL GLY VAL ASN LYS SEQRES 20 A 295 ASN ILE PHE LEU LYS ASP GLN ASP ILE PHE VAL GLN LYS SEQRES 21 A 295 LEU LEU ASP GLN VAL SER ALA GLU ASP LEU ALA ALA GLU SEQRES 22 A 295 LYS LYS ARG ILE MET HIS CYS LEU GLY LEU ALA SER ASP SEQRES 23 A 295 ILE GLN LYS LEU CYS HIS GLN LYS LYS FORMUL 2 HOH *294(H2 O) HELIX 1 1 GLY A 17 LYS A 28 1 12 HELIX 2 2 ASP A 29 ALA A 34 1 6 HELIX 3 3 SER A 57 SER A 64 1 8 HELIX 4 4 GLU A 75 SER A 77 5 3 HELIX 5 5 SER A 78 ALA A 89 1 12 HELIX 6 6 SER A 102 GLY A 117 1 16 HELIX 7 7 HIS A 124 LEU A 128 5 5 HELIX 8 8 MET A 129 LEU A 140 1 12 HELIX 9 9 GLU A 157 GLY A 162 1 6 HELIX 10 10 PHE A 163 GLY A 168 1 6 HELIX 11 11 GLY A 168 GLY A 180 1 13 HELIX 12 12 LYS A 193 GLN A 196 5 4 HELIX 13 13 ASN A 248 LEU A 262 1 15 HELIX 14 14 SER A 266 HIS A 292 1 27 SHEET 1 A 5 LEU A 36 VAL A 42 0 SHEET 2 A 5 PHE A 9 VAL A 14 1 O PHE A 9 N ASN A 37 SHEET 3 A 5 VAL A 69 ILE A 72 1 N VAL A 69 O GLY A 10 SHEET 4 A 5 HIS A 92 GLU A 96 1 O HIS A 92 N ALA A 70 SHEET 5 A 5 LEU A 120 GLU A 123 1 O HIS A 121 N VAL A 95 SHEET 1 B 2 SER A 49 LEU A 50 0 SHEET 2 B 2 VAL A 53 ARG A 54 -1 N VAL A 53 O LEU A 50 SHEET 1 C 6 SER A 183 ARG A 192 0 SHEET 2 C 6 TYR A 197 GLU A 205 -1 O TYR A 197 N ARG A 192 SHEET 3 C 6 LEU A 211 LYS A 218 -1 N LEU A 212 O LEU A 204 SHEET 4 C 6 LEU A 144 ALA A 153 1 O LEU A 145 N LEU A 211 SHEET 5 C 6 ASN A 225 PHE A 232 -1 O ASN A 225 N THR A 152 SHEET 6 C 6 GLY A 235 LEU A 237 -1 O GLY A 235 N PHE A 232 CISPEP 1 TYR A 97 PRO A 98 0 -1.37 CRYST1 58.682 70.487 87.866 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 0.017041 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011381 0.00000