PDB Short entry for 2D0U HEADER OXIDOREDUCTASE 08-AUG-05 2D0U TITLE CRYSTAL STRUCTURE OF CYANIDE BOUND FORM OF HUMAN INDOLEAMINE 2,3- TITLE 2 DIOXYGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INDOLEAMINE 2,3-DIOXYGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: IDO, INDOLEAMINE-PYRROLE 2,3-DIOXYGENASE; COMPND 5 EC: 1.13.11.42; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODONPLUS-RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HELIX BUNDLE, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 2 STRUCTURAL GENOMICS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.SUGIMOTO,S.ODA,T.OTSUKI,T.HINO,T.YOSHIDA,Y.SHIRO,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 5 25-OCT-23 2D0U 1 REMARK SEQADV LINK REVDAT 4 11-OCT-17 2D0U 1 REMARK REVDAT 3 24-FEB-09 2D0U 1 VERSN REVDAT 2 16-MAY-06 2D0U 1 JRNL REVDAT 1 31-JAN-06 2D0U 0 JRNL AUTH H.SUGIMOTO,S.ODA,T.OTSUKI,T.HINO,T.YOSHIDA,Y.SHIRO JRNL TITL CRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE: JRNL TITL 2 CATALYTIC MECHANISM OF O2 INCORPORATION BY A HEME-CONTAINING JRNL TITL 3 DIOXYGENASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 2611 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16477023 JRNL DOI 10.1073/PNAS.0508996103 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 3.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2248730.300 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 14422 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) : 0.213 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 718 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.61 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2274 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 104 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5920 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 142 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -14.09000 REMARK 3 B22 (A**2) : -1.69000 REMARK 3 B33 (A**2) : 15.79000 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) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.49 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.56 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.920 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.24 REMARK 3 BSOL : 10.00 REMARK 3 REMARK 3 NCS MODEL : CONSTR REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; 400 REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; 2 REMARK 3 GROUP 2 POSITIONAL (A) : NULL ; 100 REMARK 3 GROUP 2 B-FACTOR (A**2) : NULL ; 4 REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2D0U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000024847. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 0.9785 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14518 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : 0.09600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.34100 REMARK 200 R SYM FOR SHELL (I) : 0.34100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 2D0T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, CHES, AMMONIUM ACETATE, PH REMARK 280 9.0, VAPOR DIFFUSION, HANGING 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 43.17600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.68900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.54450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.68900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.17600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.54450 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: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 HIS A 3 REMARK 465 ALA A 4 REMARK 465 MET A 5 REMARK 465 GLU A 6 REMARK 465 ASN A 7 REMARK 465 SER A 8 REMARK 465 TRP A 9 REMARK 465 THR A 10 REMARK 465 ILE A 11 REMARK 465 GLN A 361 REMARK 465 PRO A 362 REMARK 465 LYS A 363 REMARK 465 GLU A 364 REMARK 465 ASN A 365 REMARK 465 LYS A 366 REMARK 465 THR A 367 REMARK 465 SER A 368 REMARK 465 GLU A 369 REMARK 465 ASP A 370 REMARK 465 PRO A 371 REMARK 465 SER A 372 REMARK 465 LYS A 373 REMARK 465 LEU A 374 REMARK 465 GLU A 375 REMARK 465 ALA A 376 REMARK 465 LYS A 377 REMARK 465 GLY A 378 REMARK 465 THR A 379 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 HIS B 3 REMARK 465 ALA B 4 REMARK 465 MET B 5 REMARK 465 GLU B 6 REMARK 465 ASN B 7 REMARK 465 SER B 8 REMARK 465 TRP B 9 REMARK 465 THR B 10 REMARK 465 GLN B 361 REMARK 465 PRO B 362 REMARK 465 LYS B 363 REMARK 465 GLU B 364 REMARK 465 ASN B 365 REMARK 465 LYS B 366 REMARK 465 THR B 367 REMARK 465 SER B 368 REMARK 465 GLU B 369 REMARK 465 ASP B 370 REMARK 465 PRO B 371 REMARK 465 SER B 372 REMARK 465 LYS B 373 REMARK 465 LEU B 374 REMARK 465 GLU B 375 REMARK 465 ALA B 376 REMARK 465 LYS B 377 REMARK 465 GLY B 378 REMARK 465 THR B 379 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 LYS B 323 N ASP B 325 2.00 REMARK 500 O LYS A 323 N ASP A 325 2.09 REMARK 500 NH2 ARG B 80 O PRO B 121 2.11 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 NH2 ARG A 100 OE1 GLU B 402 3655 2.08 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 ARG A 80 CZ ARG A 80 NH1 -0.086 REMARK 500 GLU A 146 CD GLU A 146 OE1 -0.076 REMARK 500 GLU A 202 CD GLU A 202 OE1 -0.078 REMARK 500 LYS A 323 C LYS A 323 O -0.163 REMARK 500 ARG B 80 CZ ARG B 80 NH1 -0.083 REMARK 500 GLU B 146 CD GLU B 146 OE1 -0.081 REMARK 500 GLU B 202 CD GLU B 202 OE1 -0.078 REMARK 500 SER B 244 CB SER B 244 OG -0.083 REMARK 500 LYS B 323 C LYS B 323 O -0.158 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 80 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 58 NE - CZ - NH1 ANGL. DEV. = -4.7 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 LYS A 13 -155.10 -79.13 REMARK 500 GLU A 14 39.85 -69.58 REMARK 500 ASN A 27 71.76 37.96 REMARK 500 ASP A 128 -66.64 -90.47 REMARK 500 VAL A 130 -72.50 -127.35 REMARK 500 ASN A 133 64.45 -102.07 REMARK 500 VAL A 229 -75.91 -120.47 REMARK 500 LEU A 243 39.87 -145.67 REMARK 500 SER A 244 -57.21 -20.59 REMARK 500 ILE A 354 -62.93 -145.37 REMARK 500 LYS A 401 40.98 -91.94 REMARK 500 LYS B 13 -141.10 -84.64 REMARK 500 HIS B 16 61.34 64.05 REMARK 500 ASN B 27 75.23 34.17 REMARK 500 ASP B 128 -66.27 -91.65 REMARK 500 VAL B 130 -72.61 -127.14 REMARK 500 ASN B 133 61.24 -101.01 REMARK 500 VAL B 229 -75.98 -120.06 REMARK 500 LEU B 243 37.68 -144.49 REMARK 500 SER B 244 -63.91 -11.61 REMARK 500 ILE B 354 -62.65 -144.46 REMARK 500 REMARK 500 REMARK: NULL 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 HEM A 404 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 346 NE2 REMARK 620 2 HEM A 404 NA 94.4 REMARK 620 3 HEM A 404 NB 96.9 88.7 REMARK 620 4 HEM A 404 NC 90.4 172.8 85.4 REMARK 620 5 HEM A 404 ND 87.1 94.6 174.5 90.9 REMARK 620 6 CYN A 405 C 174.9 86.7 88.1 89.0 87.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 404 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 346 NE2 REMARK 620 2 HEM B 404 NA 94.4 REMARK 620 3 HEM B 404 NB 98.0 87.0 REMARK 620 4 HEM B 404 NC 89.0 172.9 86.3 REMARK 620 5 HEM B 404 ND 84.5 94.0 177.2 92.6 REMARK 620 6 CYN B1405 C 174.8 86.1 76.8 90.0 100.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CYN A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CYN B 1405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHE A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHE A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHE B 1406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHE B 1407 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D0T RELATED DB: PDB REMARK 900 LIGAND WAS EXCHANGED FROM CYANIDE TO PHENYLIMIDAZOLE BY SORKING REMARK 900 CRYSTAL. REMARK 900 RELATED ID: MY_001000021.2 RELATED DB: TARGETDB DBREF 2D0U A 1 403 UNP P14902 I23O_HUMAN 1 403 DBREF 2D0U B 1 403 UNP P14902 I23O_HUMAN 1 403 SEQADV 2D0U GLY A -2 UNP P14902 CLONING ARTIFACT SEQADV 2D0U SER A -1 UNP P14902 CLONING ARTIFACT SEQADV 2D0U HIS A 0 UNP P14902 CLONING ARTIFACT SEQADV 2D0U GLY B -2 UNP P14902 CLONING ARTIFACT SEQADV 2D0U SER B -1 UNP P14902 CLONING ARTIFACT SEQADV 2D0U HIS B 0 UNP P14902 CLONING ARTIFACT SEQRES 1 A 406 GLY SER HIS MET ALA HIS ALA MET GLU ASN SER TRP THR SEQRES 2 A 406 ILE SER LYS GLU TYR HIS ILE ASP GLU GLU VAL GLY PHE SEQRES 3 A 406 ALA LEU PRO ASN PRO GLN GLU ASN LEU PRO ASP PHE TYR SEQRES 4 A 406 ASN ASP TRP MET PHE ILE ALA LYS HIS LEU PRO ASP LEU SEQRES 5 A 406 ILE GLU SER GLY GLN LEU ARG GLU ARG VAL GLU LYS LEU SEQRES 6 A 406 ASN MET LEU SER ILE ASP HIS LEU THR ASP HIS LYS SER SEQRES 7 A 406 GLN ARG LEU ALA ARG LEU VAL LEU GLY CYS ILE THR MET SEQRES 8 A 406 ALA TYR VAL TRP GLY LYS GLY HIS GLY ASP VAL ARG LYS SEQRES 9 A 406 VAL LEU PRO ARG ASN ILE ALA VAL PRO TYR CYS GLN LEU SEQRES 10 A 406 SER LYS LYS LEU GLU LEU PRO PRO ILE LEU VAL TYR ALA SEQRES 11 A 406 ASP CYS VAL LEU ALA ASN TRP LYS LYS LYS ASP PRO ASN SEQRES 12 A 406 LYS PRO LEU THR TYR GLU ASN MET ASP VAL LEU PHE SER SEQRES 13 A 406 PHE ARG ASP GLY ASP CYS SER LYS GLY PHE PHE LEU VAL SEQRES 14 A 406 SER LEU LEU VAL GLU ILE ALA ALA ALA SER ALA ILE LYS SEQRES 15 A 406 VAL ILE PRO THR VAL PHE LYS ALA MET GLN MET GLN GLU SEQRES 16 A 406 ARG ASP THR LEU LEU LYS ALA LEU LEU GLU ILE ALA SER SEQRES 17 A 406 CYS LEU GLU LYS ALA LEU GLN VAL PHE HIS GLN ILE HIS SEQRES 18 A 406 ASP HIS VAL ASN PRO LYS ALA PHE PHE SER VAL LEU ARG SEQRES 19 A 406 ILE TYR LEU SER GLY TRP LYS GLY ASN PRO GLN LEU SER SEQRES 20 A 406 ASP GLY LEU VAL TYR GLU GLY PHE TRP GLU ASP PRO LYS SEQRES 21 A 406 GLU PHE ALA GLY GLY SER ALA GLY GLN SER SER VAL PHE SEQRES 22 A 406 GLN CYS PHE ASP VAL LEU LEU GLY ILE GLN GLN THR ALA SEQRES 23 A 406 GLY GLY GLY HIS ALA ALA GLN PHE LEU GLN ASP MET ARG SEQRES 24 A 406 ARG TYR MET PRO PRO ALA HIS ARG ASN PHE LEU CYS SER SEQRES 25 A 406 LEU GLU SER ASN PRO SER VAL ARG GLU PHE VAL LEU SER SEQRES 26 A 406 LYS GLY ASP ALA GLY LEU ARG GLU ALA TYR ASP ALA CYS SEQRES 27 A 406 VAL LYS ALA LEU VAL SER LEU ARG SER TYR HIS LEU GLN SEQRES 28 A 406 ILE VAL THR LYS TYR ILE LEU ILE PRO ALA SER GLN GLN SEQRES 29 A 406 PRO LYS GLU ASN LYS THR SER GLU ASP PRO SER LYS LEU SEQRES 30 A 406 GLU ALA LYS GLY THR GLY GLY THR ASP LEU MET ASN PHE SEQRES 31 A 406 LEU LYS THR VAL ARG SER THR THR GLU LYS SER LEU LEU SEQRES 32 A 406 LYS GLU GLY SEQRES 1 B 406 GLY SER HIS MET ALA HIS ALA MET GLU ASN SER TRP THR SEQRES 2 B 406 ILE SER LYS GLU TYR HIS ILE ASP GLU GLU VAL GLY PHE SEQRES 3 B 406 ALA LEU PRO ASN PRO GLN GLU ASN LEU PRO ASP PHE TYR SEQRES 4 B 406 ASN ASP TRP MET PHE ILE ALA LYS HIS LEU PRO ASP LEU SEQRES 5 B 406 ILE GLU SER GLY GLN LEU ARG GLU ARG VAL GLU LYS LEU SEQRES 6 B 406 ASN MET LEU SER ILE ASP HIS LEU THR ASP HIS LYS SER SEQRES 7 B 406 GLN ARG LEU ALA ARG LEU VAL LEU GLY CYS ILE THR MET SEQRES 8 B 406 ALA TYR VAL TRP GLY LYS GLY HIS GLY ASP VAL ARG LYS SEQRES 9 B 406 VAL LEU PRO ARG ASN ILE ALA VAL PRO TYR CYS GLN LEU SEQRES 10 B 406 SER LYS LYS LEU GLU LEU PRO PRO ILE LEU VAL TYR ALA SEQRES 11 B 406 ASP CYS VAL LEU ALA ASN TRP LYS LYS LYS ASP PRO ASN SEQRES 12 B 406 LYS PRO LEU THR TYR GLU ASN MET ASP VAL LEU PHE SER SEQRES 13 B 406 PHE ARG ASP GLY ASP CYS SER LYS GLY PHE PHE LEU VAL SEQRES 14 B 406 SER LEU LEU VAL GLU ILE ALA ALA ALA SER ALA ILE LYS SEQRES 15 B 406 VAL ILE PRO THR VAL PHE LYS ALA MET GLN MET GLN GLU SEQRES 16 B 406 ARG ASP THR LEU LEU LYS ALA LEU LEU GLU ILE ALA SER SEQRES 17 B 406 CYS LEU GLU LYS ALA LEU GLN VAL PHE HIS GLN ILE HIS SEQRES 18 B 406 ASP HIS VAL ASN PRO LYS ALA PHE PHE SER VAL LEU ARG SEQRES 19 B 406 ILE TYR LEU SER GLY TRP LYS GLY ASN PRO GLN LEU SER SEQRES 20 B 406 ASP GLY LEU VAL TYR GLU GLY PHE TRP GLU ASP PRO LYS SEQRES 21 B 406 GLU PHE ALA GLY GLY SER ALA GLY GLN SER SER VAL PHE SEQRES 22 B 406 GLN CYS PHE ASP VAL LEU LEU GLY ILE GLN GLN THR ALA SEQRES 23 B 406 GLY GLY GLY HIS ALA ALA GLN PHE LEU GLN ASP MET ARG SEQRES 24 B 406 ARG TYR MET PRO PRO ALA HIS ARG ASN PHE LEU CYS SER SEQRES 25 B 406 LEU GLU SER ASN PRO SER VAL ARG GLU PHE VAL LEU SER SEQRES 26 B 406 LYS GLY ASP ALA GLY LEU ARG GLU ALA TYR ASP ALA CYS SEQRES 27 B 406 VAL LYS ALA LEU VAL SER LEU ARG SER TYR HIS LEU GLN SEQRES 28 B 406 ILE VAL THR LYS TYR ILE LEU ILE PRO ALA SER GLN GLN SEQRES 29 B 406 PRO LYS GLU ASN LYS THR SER GLU ASP PRO SER LYS LEU SEQRES 30 B 406 GLU ALA LYS GLY THR GLY GLY THR ASP LEU MET ASN PHE SEQRES 31 B 406 LEU LYS THR VAL ARG SER THR THR GLU LYS SER LEU LEU SEQRES 32 B 406 LYS GLU GLY HET CYN A 405 2 HET HEM A 404 43 HET NHE A 406 13 HET NHE A 407 13 HET CYN B1405 2 HET HEM B 404 43 HET NHE B1406 13 HET NHE B1407 13 HETNAM CYN CYANIDE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID HETSYN HEM HEME HETSYN NHE N-CYCLOHEXYLTAURINE; CHES FORMUL 3 CYN 2(C N 1-) FORMUL 4 HEM 2(C34 H32 FE N4 O4) FORMUL 5 NHE 4(C8 H17 N O3 S) HELIX 1 1 PRO A 33 PHE A 35 5 3 HELIX 2 2 TYR A 36 HIS A 45 1 10 HELIX 3 3 HIS A 45 SER A 52 1 8 HELIX 4 4 GLN A 54 LYS A 61 1 8 HELIX 5 5 ASP A 72 GLY A 93 1 22 HELIX 6 6 PRO A 104 GLU A 119 1 16 HELIX 7 7 VAL A 125 VAL A 130 1 6 HELIX 8 8 THR A 144 GLU A 146 5 3 HELIX 9 9 CYS A 159 LYS A 179 1 21 HELIX 10 10 VAL A 180 MET A 190 1 11 HELIX 11 11 GLU A 192 HIS A 215 1 24 HELIX 12 12 GLN A 216 VAL A 221 1 6 HELIX 13 13 ASN A 222 VAL A 229 1 8 HELIX 14 14 VAL A 229 LEU A 234 1 6 HELIX 15 15 ASN A 240 SER A 244 5 5 HELIX 16 16 SER A 263 GLN A 266 5 4 HELIX 17 17 SER A 267 LEU A 277 1 11 HELIX 18 18 GLY A 286 ARG A 296 1 11 HELIX 19 19 ARG A 297 MET A 299 5 3 HELIX 20 20 PRO A 300 SER A 312 1 13 HELIX 21 21 SER A 315 SER A 322 1 8 HELIX 22 22 ASP A 325 ILE A 354 1 30 HELIX 23 23 ILE A 354 SER A 359 1 6 HELIX 24 24 GLY A 381 SER A 398 1 18 HELIX 25 25 PRO B 33 PHE B 35 5 3 HELIX 26 26 TYR B 36 HIS B 45 1 10 HELIX 27 27 HIS B 45 SER B 52 1 8 HELIX 28 28 GLN B 54 LYS B 61 1 8 HELIX 29 29 ASP B 72 GLY B 93 1 22 HELIX 30 30 PRO B 104 GLU B 119 1 16 HELIX 31 31 VAL B 125 VAL B 130 1 6 HELIX 32 32 THR B 144 GLU B 146 5 3 HELIX 33 33 CYS B 159 LYS B 179 1 21 HELIX 34 34 VAL B 180 MET B 190 1 11 HELIX 35 35 GLU B 192 HIS B 215 1 24 HELIX 36 36 GLN B 216 VAL B 221 1 6 HELIX 37 37 ASN B 222 VAL B 229 1 8 HELIX 38 38 VAL B 229 LEU B 234 1 6 HELIX 39 39 ASN B 240 SER B 244 5 5 HELIX 40 40 SER B 263 GLN B 266 5 4 HELIX 41 41 SER B 267 LEU B 277 1 11 HELIX 42 42 GLY B 286 ARG B 296 1 11 HELIX 43 43 ARG B 297 MET B 299 5 3 HELIX 44 44 PRO B 300 SER B 312 1 13 HELIX 45 45 SER B 315 SER B 322 1 8 HELIX 46 46 ASP B 325 ILE B 354 1 30 HELIX 47 47 ILE B 354 SER B 359 1 6 HELIX 48 48 GLY B 381 SER B 398 1 18 SHEET 1 A 2 VAL A 102 LEU A 103 0 SHEET 2 A 2 VAL A 248 TYR A 249 1 O VAL A 248 N LEU A 103 SHEET 1 B 2 LYS A 135 LYS A 136 0 SHEET 2 B 2 MET A 148 ASP A 149 -1 O ASP A 149 N LYS A 135 SHEET 1 C 2 VAL B 102 LEU B 103 0 SHEET 2 C 2 VAL B 248 TYR B 249 1 O VAL B 248 N LEU B 103 SHEET 1 D 2 LYS B 135 LYS B 136 0 SHEET 2 D 2 MET B 148 ASP B 149 -1 O ASP B 149 N LYS B 135 SSBOND 1 CYS A 308 CYS B 308 1555 1555 2.04 LINK NE2 HIS A 346 FE HEM A 404 1555 1555 1.98 LINK FE HEM A 404 C CYN A 405 1555 1555 2.01 LINK NE2 HIS B 346 FE HEM B 404 1555 1555 2.00 LINK FE HEM B 404 C CYN B1405 1555 1555 2.02 SITE 1 AC1 4 SER A 263 ALA A 264 HEM A 404 NHE A 406 SITE 1 AC2 3 SER B 263 ALA B 264 HEM B 404 SITE 1 AC3 16 PHE A 163 SER A 167 VAL A 170 PHE A 214 SITE 2 AC3 16 PHE A 226 SER A 263 ALA A 264 GLY A 265 SITE 3 AC3 16 ARG A 343 HIS A 346 ILE A 349 LEU A 384 SITE 4 AC3 16 VAL A 391 CYN A 405 NHE A 406 NHE A 407 SITE 1 AC4 7 GLY A 236 GLY A 261 GLY A 262 SER A 263 SITE 2 AC4 7 HEM A 404 CYN A 405 NHE A 407 SITE 1 AC5 6 ARG A 231 HIS A 287 PHE A 291 LEU A 384 SITE 2 AC5 6 HEM A 404 NHE A 406 SITE 1 AC6 20 PHE B 163 SER B 167 VAL B 170 PHE B 214 SITE 2 AC6 20 PHE B 226 SER B 263 ALA B 264 GLY B 265 SITE 3 AC6 20 PHE B 270 PHE B 291 ARG B 343 HIS B 346 SITE 4 AC6 20 ILE B 349 TYR B 353 ILE B 354 LEU B 384 SITE 5 AC6 20 VAL B 391 CYN B1405 NHE B1406 NHE B1407 SITE 1 AC7 8 PHE B 226 SER B 235 GLY B 236 GLY B 261 SITE 2 AC7 8 GLY B 262 SER B 263 HEM B 404 NHE B1407 SITE 1 AC8 5 ARG B 231 HIS B 287 LEU B 384 HEM B 404 SITE 2 AC8 5 NHE B1406 CRYST1 86.352 97.089 129.378 90.00 90.00 90.00 P 21 21 21 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 0.011581 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010300 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007729 0.00000