PDB Short entry for 4U72 HEADER OXIDOREDUCTASE 30-JUL-14 4U72 TITLE CRYSTAL STRUCTURE OF 4-PHENYLIMIDAZOLE BOUND FORM OF HUMAN INDOLEAMINE TITLE 2 2,3-DIOXYGENASE (A260G MUTANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: INDOLEAMINE 2,3-DIOXYGENASE 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: INDOLEAMINE 2,3-DIOXYGENASE; COMPND 5 SYNONYM: IDO-1,INDOLEAMINE-PYRROLE 2,3-DIOXYGENASE; COMPND 6 EC: 1.13.11.52; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IDO1, IDO, INDO; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODONPLUS RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-15B KEYWDS METAL-BINDING, ALL ALPHA, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.SUGIMOTO,M.HORITANI,E.KOMETANI,Y.SHIRO REVDAT 2 29-JAN-20 4U72 1 REMARK REVDAT 1 02-SEP-15 4U72 0 JRNL AUTH M.HORITANI,E.KOMETANI,E.VOTTERO,T.OTSUKI,Y.SHIRO,H.SUGIMOTO JRNL TITL CONFORMATION AND MOBILITY OF ACTIVE SITE LOOP IS CRITICAL JRNL TITL 2 FOR SUBSTRATE BINDING AND INHIBITION IN HUMAN INDOLEAMINE JRNL TITL 3 2,3-DIOXYGENASE JRNL REF TO BE PUBLISHED REF NOW ASSIGNED AS JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.SUGIMOTO,S.ODA,T.OTSUKI,T.HINO,T.YOSHIDA,Y.SHIRO REMARK 1 TITL CRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE: REMARK 1 TITL 2 CATALYTIC MECHANISM OF O2 INCORPORATION BY A HEME-CONTAINING REMARK 1 TITL 3 DIOXYGENASE. REMARK 1 REF PROC. NATL. ACAD. SCI. V. 103 2611 2006 REMARK 1 REF 2 U.S.A. REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 16477023 REMARK 1 DOI 10.1073/PNAS.0508996103 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 74117 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3642 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3553 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 165 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5934 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 160 REMARK 3 SOLVENT ATOMS : 335 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.38000 REMARK 3 B22 (A**2) : 0.54000 REMARK 3 B33 (A**2) : -0.15000 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): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.144 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.474 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6294 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8541 ; 2.034 ; 2.005 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 753 ; 5.706 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 272 ;36.445 ;24.191 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1077 ;15.851 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;16.877 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 923 ; 0.151 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4704 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 12 403 B 12 403 477 0.120 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT U VALUES REMARK 4 REMARK 4 4U72 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000202917. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76205 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : 0.05400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 37.0330 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 (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.46400 REMARK 200 R SYM FOR SHELL (I) : 0.46400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.750 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12 % (W/V) PEG 8000, 0.2 M AMMONIUM REMARK 280 ACETATE, 1 MM 4-PHENYLIMIDAZOLE, 0.1 M CHES, PH 9.1, VAPOR REMARK 280 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 42.98550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.79100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.44500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.79100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.98550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.44500 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 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 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: 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 TYR B 298 CG TYR B 298 CD1 0.078 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 ASP A 149 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 317 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG B 100 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B 317 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP B 325 CB - CG - OD1 ANGL. DEV. = 5.8 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 ASN A 27 72.82 38.30 REMARK 500 ILE A 354 -51.51 -124.40 REMARK 500 GLU A 402 94.91 -61.81 REMARK 500 ASN B 27 73.63 34.89 REMARK 500 ASN B 27 72.83 35.78 REMARK 500 VAL B 130 -62.09 -107.85 REMARK 500 ASN B 133 53.83 -109.06 REMARK 500 VAL B 229 -63.15 -122.19 REMARK 500 LEU B 243 59.67 -143.96 REMARK 500 ILE B 354 -54.89 -125.90 REMARK 500 GLU B 402 125.43 -38.06 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 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 346 NE2 REMARK 620 2 HEM A 501 NA 89.1 REMARK 620 3 HEM A 501 NB 91.1 91.5 REMARK 620 4 HEM A 501 NC 92.0 178.9 88.7 REMARK 620 5 HEM A 501 ND 87.8 88.9 178.9 90.9 REMARK 620 6 PIM A 502 N3 176.1 87.6 91.1 91.3 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 346 NE2 REMARK 620 2 HEM B 501 NA 90.7 REMARK 620 3 HEM B 501 NB 89.5 91.6 REMARK 620 4 HEM B 501 NC 91.3 178.0 88.3 REMARK 620 5 HEM B 501 ND 89.9 88.3 179.4 91.9 REMARK 620 6 PIM B 502 N3 179.3 88.7 90.2 89.3 90.3 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 HEM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PIM A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NHE A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NHE A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PIM B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NHE B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NHE B 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D0T RELATED DB: PDB REMARK 900 WILD TYPE ENZYME DBREF 4U72 A 1 403 UNP P14902 I23O1_HUMAN 1 403 DBREF 4U72 B 1 403 UNP P14902 I23O1_HUMAN 1 403 SEQADV 4U72 GLY A -2 UNP P14902 EXPRESSION TAG SEQADV 4U72 SER A -1 UNP P14902 EXPRESSION TAG SEQADV 4U72 HIS A 0 UNP P14902 EXPRESSION TAG SEQADV 4U72 GLY A 260 UNP P14902 ALA 260 ENGINEERED MUTATION SEQADV 4U72 GLY B -2 UNP P14902 EXPRESSION TAG SEQADV 4U72 SER B -1 UNP P14902 EXPRESSION TAG SEQADV 4U72 HIS B 0 UNP P14902 EXPRESSION TAG SEQADV 4U72 GLY B 260 UNP P14902 ALA 260 ENGINEERED MUTATION 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 GLY 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 GLY 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 HEM A 501 43 HET PIM A 502 11 HET NHE A 503 13 HET NHE A 504 26 HET HEM B 501 43 HET PIM B 502 11 HET NHE B 503 13 HET NHE B 504 26 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM PIM 4-PHENYL-1H-IMIDAZOLE HETNAM NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID HETSYN HEM HEME HETSYN NHE N-CYCLOHEXYLTAURINE; CHES FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 PIM 2(C9 H8 N2) FORMUL 5 NHE 4(C8 H17 N O3 S) FORMUL 11 HOH *335(H2 O) HELIX 1 AA1 SER A 12 HIS A 16 5 5 HELIX 2 AA2 PRO A 33 PHE A 35 5 3 HELIX 3 AA3 TYR A 36 HIS A 45 1 10 HELIX 4 AA4 HIS A 45 SER A 52 1 8 HELIX 5 AA5 GLN A 54 LEU A 62 1 9 HELIX 6 AA6 SER A 66 LEU A 70 5 5 HELIX 7 AA7 ASP A 72 GLY A 93 1 22 HELIX 8 AA8 PRO A 104 GLU A 119 1 16 HELIX 9 AA9 VAL A 125 VAL A 130 1 6 HELIX 10 AB1 THR A 144 GLU A 146 5 3 HELIX 11 AB2 CYS A 159 LYS A 179 1 21 HELIX 12 AB3 VAL A 180 MET A 190 1 11 HELIX 13 AB4 GLU A 192 HIS A 215 1 24 HELIX 14 AB5 GLN A 216 VAL A 221 1 6 HELIX 15 AB6 ASN A 222 VAL A 229 1 8 HELIX 16 AB7 VAL A 229 LEU A 234 1 6 HELIX 17 AB8 ASN A 240 SER A 244 5 5 HELIX 18 AB9 SER A 263 GLN A 266 5 4 HELIX 19 AC1 SER A 267 LEU A 277 1 11 HELIX 20 AC2 GLY A 286 ARG A 296 1 11 HELIX 21 AC3 ARG A 297 MET A 299 5 3 HELIX 22 AC4 PRO A 300 SER A 312 1 13 HELIX 23 AC5 SER A 315 SER A 322 1 8 HELIX 24 AC6 ASP A 325 ILE A 354 1 30 HELIX 25 AC7 ILE A 354 GLN A 361 1 8 HELIX 26 AC8 GLY A 381 SER A 398 1 18 HELIX 27 AC9 SER B 12 HIS B 16 5 5 HELIX 28 AD1 PRO B 33 PHE B 35 5 3 HELIX 29 AD2 TYR B 36 HIS B 45 1 10 HELIX 30 AD3 HIS B 45 SER B 52 1 8 HELIX 31 AD4 GLN B 54 LEU B 62 1 9 HELIX 32 AD5 SER B 66 LEU B 70 5 5 HELIX 33 AD6 ASP B 72 GLY B 93 1 22 HELIX 34 AD7 PRO B 104 GLU B 119 1 16 HELIX 35 AD8 VAL B 125 VAL B 130 1 6 HELIX 36 AD9 THR B 144 GLU B 146 5 3 HELIX 37 AE1 CYS B 159 SER B 176 1 18 HELIX 38 AE2 ALA B 177 LYS B 179 5 3 HELIX 39 AE3 VAL B 180 MET B 190 1 11 HELIX 40 AE4 GLU B 192 HIS B 215 1 24 HELIX 41 AE5 GLN B 216 VAL B 221 1 6 HELIX 42 AE6 ASN B 222 VAL B 229 1 8 HELIX 43 AE7 VAL B 229 SER B 235 1 7 HELIX 44 AE8 ASN B 240 SER B 244 5 5 HELIX 45 AE9 SER B 263 GLN B 266 5 4 HELIX 46 AF1 SER B 267 LEU B 277 1 11 HELIX 47 AF2 GLY B 286 ARG B 296 1 11 HELIX 48 AF3 ARG B 297 MET B 299 5 3 HELIX 49 AF4 PRO B 300 SER B 312 1 13 HELIX 50 AF5 SER B 315 LYS B 323 1 9 HELIX 51 AF6 ASP B 325 ILE B 354 1 30 HELIX 52 AF7 ILE B 354 GLN B 360 1 7 HELIX 53 AF8 GLY B 381 LYS B 397 1 17 SHEET 1 AA1 2 VAL A 102 LEU A 103 0 SHEET 2 AA1 2 VAL A 248 TYR A 249 1 O VAL A 248 N LEU A 103 SHEET 1 AA2 2 LYS A 135 LYS A 136 0 SHEET 2 AA2 2 MET A 148 ASP A 149 -1 O ASP A 149 N LYS A 135 SHEET 1 AA3 2 VAL B 102 LEU B 103 0 SHEET 2 AA3 2 VAL B 248 TYR B 249 1 O VAL B 248 N LEU B 103 SHEET 1 AA4 2 LYS B 135 LYS B 136 0 SHEET 2 AA4 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 2.08 LINK NE2 HIS A 346 FE HEM A 501 1555 1555 2.03 LINK NE2 HIS B 346 FE HEM B 501 1555 1555 2.03 LINK FE HEM A 501 N3 PIM A 502 1555 1555 1.95 LINK FE HEM B 501 N3 PIM B 502 1555 1555 1.96 SITE 1 AC1 22 TYR A 126 PHE A 163 SER A 167 PHE A 214 SITE 2 AC1 22 PHE A 226 SER A 263 ALA A 264 PHE A 270 SITE 3 AC1 22 ARG A 343 HIS A 346 ILE A 349 VAL A 350 SITE 4 AC1 22 TYR A 353 LEU A 384 LEU A 388 VAL A 391 SITE 5 AC1 22 PIM A 502 NHE A 503 NHE A 504 HOH A 619 SITE 6 AC1 22 HOH A 629 HOH A 672 SITE 1 AC2 7 VAL A 130 PHE A 163 SER A 167 SER A 263 SITE 2 AC2 7 ALA A 264 HEM A 501 NHE A 503 SITE 1 AC3 11 PHE A 163 PHE A 226 SER A 235 GLY A 236 SITE 2 AC3 11 GLY A 260 GLY A 261 GLY A 262 HEM A 501 SITE 3 AC3 11 PIM A 502 NHE A 504 HOH A 684 SITE 1 AC4 7 ARG A 231 LYS A 238 GLY A 260 HIS A 287 SITE 2 AC4 7 PHE A 291 HEM A 501 NHE A 503 SITE 1 AC5 22 PHE B 163 SER B 167 PHE B 214 PHE B 226 SITE 2 AC5 22 SER B 263 ALA B 264 PHE B 270 ARG B 343 SITE 3 AC5 22 HIS B 346 ILE B 349 VAL B 350 TYR B 353 SITE 4 AC5 22 ILE B 354 LEU B 384 LEU B 388 VAL B 391 SITE 5 AC5 22 PIM B 502 NHE B 503 NHE B 504 HOH B 632 SITE 6 AC5 22 HOH B 635 HOH B 686 SITE 1 AC6 7 VAL B 130 PHE B 163 SER B 167 SER B 263 SITE 2 AC6 7 ALA B 264 HEM B 501 NHE B 503 SITE 1 AC7 11 PHE B 163 PHE B 226 SER B 235 GLY B 236 SITE 2 AC7 11 GLY B 260 GLY B 261 GLY B 262 HEM B 501 SITE 3 AC7 11 PIM B 502 NHE B 504 HOH B 671 SITE 1 AC8 10 ARG B 231 LYS B 238 GLY B 260 HIS B 287 SITE 2 AC8 10 PHE B 291 LEU B 384 PHE B 387 HEM B 501 SITE 3 AC8 10 NHE B 503 HOH B 652 CRYST1 85.971 98.890 131.582 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 0.011632 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010112 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007600 0.00000