HEADER TRANSFERASE 06-AUG-08 2VZW TITLE X-RAY STRUCTURE OF THE HEME-BOUND GAF DOMAIN OF SENSORY HISTIDINE TITLE 2 KINASE DOST OF MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE HISTIDINE KINASE RESPONSE REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: GAF SENSORY DOMAIN, RESIDUES 61-208; COMPND 5 SYNONYM: GAF FAMILY PROTEIN, DOST; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: RV2027C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET23A KEYWDS TRANSFERASE, OXYGEN BINDING, SIGNAL TRANSDUCTION EXPDTA X-RAY DIFFRACTION AUTHOR L.M.PODUST,A.IOANOVICIU,P.R.ORTIZ DE MONTELLANO REVDAT 6 08-MAY-24 2VZW 1 REMARK LINK REVDAT 5 11-MAR-20 2VZW 1 REMARK REVDAT 4 07-FEB-18 2VZW 1 JRNL REVDAT 3 06-MAR-13 2VZW 1 REMARK REVDAT 2 13-JUL-11 2VZW 1 VERSN REVDAT 1 17-MAR-09 2VZW 0 JRNL AUTH L.M.PODUST,A.IOANOVICIU,P.R.ORTIZ DE MONTELLANO JRNL TITL 2.3 A X-RAY STRUCTURE OF THE HEME-BOUND GAF DOMAIN OF JRNL TITL 2 SENSORY HISTIDINE KINASE DOST OF MYCOBACTERIUM TUBERCULOSIS. JRNL REF BIOCHEMISTRY V. 47 12523 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18980385 JRNL DOI 10.1021/BI8012356 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 88.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21731 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) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1171 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1605 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2262 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 109 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 53.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.86000 REMARK 3 B22 (A**2) : -0.86000 REMARK 3 B33 (A**2) : 1.73000 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): 0.257 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.231 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.201 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.500 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2467 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3388 ; 2.288 ; 2.083 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 303 ; 8.875 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;38.982 ;22.632 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 362 ;20.569 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;22.484 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 360 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1962 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1222 ; 0.257 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1653 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 134 ; 0.246 ; 0.200 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): 49 ; 0.274 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.176 ; 0.200 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): 1544 ; 0.861 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2401 ; 1.429 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1043 ; 2.490 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 983 ; 3.677 ; 4.500 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 61 A 205 REMARK 3 ORIGIN FOR THE GROUP (A): -11.9720 17.2460 60.2240 REMARK 3 T TENSOR REMARK 3 T11: -0.1452 T22: -0.1881 REMARK 3 T33: -0.0673 T12: 0.0284 REMARK 3 T13: -0.0453 T23: -0.0366 REMARK 3 L TENSOR REMARK 3 L11: 3.8502 L22: 4.9281 REMARK 3 L33: 1.7590 L12: -0.9378 REMARK 3 L13: 0.4228 L23: 1.6244 REMARK 3 S TENSOR REMARK 3 S11: -0.0160 S12: 0.0787 S13: 0.2066 REMARK 3 S21: 0.0257 S22: -0.0053 S23: -0.0759 REMARK 3 S31: -0.1576 S32: -0.0777 S33: 0.0213 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 60 B 208 REMARK 3 ORIGIN FOR THE GROUP (A): -27.8970 30.9160 79.2980 REMARK 3 T TENSOR REMARK 3 T11: -0.2274 T22: -0.1582 REMARK 3 T33: -0.0678 T12: 0.0333 REMARK 3 T13: 0.0043 T23: 0.0153 REMARK 3 L TENSOR REMARK 3 L11: 3.6014 L22: 3.6494 REMARK 3 L33: 2.8262 L12: -0.1754 REMARK 3 L13: -1.5943 L23: -0.0205 REMARK 3 S TENSOR REMARK 3 S11: -0.1454 S12: -0.0570 S13: -0.0294 REMARK 3 S21: 0.1073 S22: 0.1422 S23: -0.0993 REMARK 3 S31: 0.0871 S32: 0.2864 S33: 0.0031 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1206 A 1206 REMARK 3 ORIGIN FOR THE GROUP (A): -10.2930 9.4480 56.3400 REMARK 3 T TENSOR REMARK 3 T11: -0.1148 T22: -0.0504 REMARK 3 T33: 0.1619 T12: 0.0204 REMARK 3 T13: -0.0524 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 11.2038 L22: 8.3719 REMARK 3 L33: 4.0436 L12: -2.6864 REMARK 3 L13: -1.3246 L23: 5.7983 REMARK 3 S TENSOR REMARK 3 S11: 0.0441 S12: 0.7999 S13: 0.9072 REMARK 3 S21: -0.4147 S22: 0.3117 S23: -0.0384 REMARK 3 S31: 0.3894 S32: -0.2691 S33: -0.3558 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1209 B 1209 REMARK 3 ORIGIN FOR THE GROUP (A): -35.1980 33.2160 84.1540 REMARK 3 T TENSOR REMARK 3 T11: -0.1241 T22: -0.1354 REMARK 3 T33: 0.0886 T12: 0.0543 REMARK 3 T13: 0.1598 T23: 0.1663 REMARK 3 L TENSOR REMARK 3 L11: 14.9922 L22: 5.4869 REMARK 3 L33: 4.2520 L12: -8.8503 REMARK 3 L13: -4.3397 L23: 3.4482 REMARK 3 S TENSOR REMARK 3 S11: -0.6879 S12: -0.3545 S13: -0.0598 REMARK 3 S21: 0.5980 S22: 0.1372 S23: 0.7384 REMARK 3 S31: 0.0476 S32: 0.1361 S33: 0.5507 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 ADDED IN THE RIDING REMARK 3 POSITIONS. DISORDERED REGIONS WERE OMITTED FROM THE STRUCTURE REMARK 4 REMARK 4 2VZW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1290037123. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11587, 1.73989, 1.65312 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22939 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 47.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: ELVES REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% TACSIMATE, PH 6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 33.38000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.07000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.69000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLU A 206 REMARK 465 SER A 207 REMARK 465 ARG A 208 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 GLU A 124 CG CD OE1 OE2 REMARK 470 GLU A 205 CG CD OE1 OE2 REMARK 470 GLU B 104 CG CD OE1 OE2 REMARK 470 LYS B 127 CG CD CE NZ 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 NH2 ARG A 116 O HOH A 2024 2.05 REMARK 500 O HOH A 2036 O HOH A 2037 2.07 REMARK 500 O HOH A 2003 O HOH B 2004 2.12 REMARK 500 O LEU B 203 O HOH B 2056 2.12 REMARK 500 OE1 GLU B 95 O HOH B 2012 2.13 REMARK 500 O HOH B 2040 O HOH B 2053 2.13 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 LEU A 76 CA - CB - CG ANGL. DEV. = 17.0 DEGREES REMARK 500 LEU A 84 CA - CB - CG ANGL. DEV. = 20.0 DEGREES REMARK 500 ASP A 90 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 106 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 PRO A 126 C - N - CA ANGL. DEV. = 15.6 DEGREES REMARK 500 LEU A 168 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 LEU B 119 CA - CB - CG ANGL. DEV. = -23.1 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 PRO A 126 -8.03 34.37 REMARK 500 HIS A 146 -15.80 81.92 REMARK 500 ARG A 161 -126.28 44.96 REMARK 500 ASP A 175 148.74 48.60 REMARK 500 ARG A 202 -108.18 82.88 REMARK 500 LEU A 203 -40.18 96.65 REMARK 500 LYS B 61 -8.33 77.33 REMARK 500 ASP B 102 -168.93 -65.43 REMARK 500 THR B 105 -71.69 84.64 REMARK 500 PRO B 126 -139.33 -28.20 REMARK 500 LYS B 127 142.30 44.31 REMARK 500 PRO B 138 -7.49 -58.34 REMARK 500 SER B 140 124.27 -28.55 REMARK 500 HIS B 146 -17.82 85.76 REMARK 500 ARG B 151 -58.57 -123.14 REMARK 500 ARG B 161 -124.85 60.30 REMARK 500 GLU B 172 49.60 73.78 REMARK 500 GLN B 177 150.44 -44.62 REMARK 500 SER B 207 -23.60 -166.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 125 PRO A 126 85.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 OXYGEN (OXY): COORDINATION BOND TO THE HEME IRON REMARK 600 PROTOPORPHYRIN IX CONTAINING FE (HEM): COORDINATION BOND REMARK 600 BETWEEN FE AND HIS 147 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 A1206 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 147 NE2 REMARK 620 2 HEM A1206 NA 92.0 REMARK 620 3 HEM A1206 NB 91.2 88.2 REMARK 620 4 HEM A1206 NC 93.8 173.8 89.5 REMARK 620 5 HEM A1206 ND 94.1 91.8 174.7 90.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B1209 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 147 NE2 REMARK 620 2 HEM B1209 NA 95.7 REMARK 620 3 HEM B1209 NB 91.3 92.7 REMARK 620 4 HEM B1209 NC 88.7 174.8 89.7 REMARK 620 5 HEM B1209 ND 93.9 90.9 173.4 86.2 REMARK 620 6 OXY B1210 O2 173.2 78.7 85.1 97.0 90.2 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 1206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 1209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXY B 1210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 1211 REMARK 999 REMARK 999 SEQUENCE REMARK 999 ENGINEERED FIRST RESIDUE GLY 60 DBREF 2VZW A 61 208 UNP O53473 DOST_MYCTU 61 208 DBREF 2VZW B 61 208 UNP O53473 DOST_MYCTU 61 208 SEQADV 2VZW GLY A 60 UNP O53473 EXPRESSION TAG SEQADV 2VZW GLY B 60 UNP O53473 EXPRESSION TAG SEQRES 1 A 149 GLY LYS LEU ASP ALA THR LEU ARG ALA ILE VAL HIS THR SEQRES 2 A 149 ALA ALA GLU LEU VAL ASP ALA ARG TYR GLY ALA LEU GLY SEQRES 3 A 149 VAL ARG GLY TYR ASP HIS ARG LEU VAL GLU PHE VAL TYR SEQRES 4 A 149 GLU GLY ILE ASP GLU GLU THR ARG HIS LEU ILE GLY SER SEQRES 5 A 149 LEU PRO GLU GLY ARG GLY VAL LEU GLY ALA LEU ILE GLU SEQRES 6 A 149 GLU PRO LYS PRO ILE ARG LEU ASP ASP ILE SER ARG HIS SEQRES 7 A 149 PRO ALA SER VAL GLY PHE PRO LEU HIS HIS PRO PRO MET SEQRES 8 A 149 ARG THR PHE LEU GLY VAL PRO VAL ARG ILE ARG ASP GLU SEQRES 9 A 149 VAL PHE GLY ASN LEU TYR LEU THR GLU LYS ALA ASP GLY SEQRES 10 A 149 GLN PRO PHE SER ASP ASP ASP GLU VAL LEU VAL GLN ALA SEQRES 11 A 149 LEU ALA ALA ALA ALA GLY ILE ALA VAL ASP ASN ALA ARG SEQRES 12 A 149 LEU PHE GLU GLU SER ARG SEQRES 1 B 149 GLY LYS LEU ASP ALA THR LEU ARG ALA ILE VAL HIS THR SEQRES 2 B 149 ALA ALA GLU LEU VAL ASP ALA ARG TYR GLY ALA LEU GLY SEQRES 3 B 149 VAL ARG GLY TYR ASP HIS ARG LEU VAL GLU PHE VAL TYR SEQRES 4 B 149 GLU GLY ILE ASP GLU GLU THR ARG HIS LEU ILE GLY SER SEQRES 5 B 149 LEU PRO GLU GLY ARG GLY VAL LEU GLY ALA LEU ILE GLU SEQRES 6 B 149 GLU PRO LYS PRO ILE ARG LEU ASP ASP ILE SER ARG HIS SEQRES 7 B 149 PRO ALA SER VAL GLY PHE PRO LEU HIS HIS PRO PRO MET SEQRES 8 B 149 ARG THR PHE LEU GLY VAL PRO VAL ARG ILE ARG ASP GLU SEQRES 9 B 149 VAL PHE GLY ASN LEU TYR LEU THR GLU LYS ALA ASP GLY SEQRES 10 B 149 GLN PRO PHE SER ASP ASP ASP GLU VAL LEU VAL GLN ALA SEQRES 11 B 149 LEU ALA ALA ALA ALA GLY ILE ALA VAL ASP ASN ALA ARG SEQRES 12 B 149 LEU PHE GLU GLU SER ARG HET HEM A1206 43 HET ACT A1207 4 HET HEM B1209 43 HET OXY B1210 2 HET ACT B1211 4 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM ACT ACETATE ION HETNAM OXY OXYGEN MOLECULE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 ACT 2(C2 H3 O2 1-) FORMUL 6 OXY O2 FORMUL 8 HOH *109(H2 O) HELIX 1 1 LYS A 61 ASP A 78 1 18 HELIX 2 2 ASP A 102 GLY A 110 1 9 HELIX 3 3 GLY A 117 GLU A 125 1 9 HELIX 4 4 ASP A 133 HIS A 137 5 5 HELIX 5 5 SER A 180 ALA A 201 1 22 HELIX 6 6 LYS B 61 VAL B 77 1 17 HELIX 7 7 ASP B 102 GLY B 110 1 9 HELIX 8 8 GLY B 117 GLU B 125 1 9 HELIX 9 9 ASP B 133 HIS B 137 5 5 HELIX 10 10 ASP B 175 GLN B 177 5 3 HELIX 11 11 SER B 180 ALA B 201 1 22 SHEET 1 AA 5 LEU A 93 GLU A 99 0 SHEET 2 AA 5 ALA A 79 ARG A 87 -1 O GLY A 82 N GLU A 99 SHEET 3 AA 5 GLU A 163 LYS A 173 -1 O PHE A 165 N ARG A 87 SHEET 4 AA 5 PHE A 153 ILE A 160 -1 O LEU A 154 N LEU A 170 SHEET 5 AA 5 ILE A 129 LEU A 131 -1 O ILE A 129 N GLY A 155 SHEET 1 BA 5 LEU B 93 GLU B 99 0 SHEET 2 BA 5 ALA B 79 ARG B 87 -1 O GLY B 82 N GLU B 99 SHEET 3 BA 5 GLU B 163 LYS B 173 -1 O PHE B 165 N ARG B 87 SHEET 4 BA 5 PHE B 153 ILE B 160 -1 O LEU B 154 N LEU B 170 SHEET 5 BA 5 ILE B 129 LEU B 131 -1 O ILE B 129 N GLY B 155 LINK NE2 HIS A 147 FE HEM A1206 1555 1555 2.14 LINK NE2 HIS B 147 FE HEM B1209 1555 1555 2.09 LINK FE HEM B1209 O2 OXY B1210 1555 1555 2.58 SITE 1 AC1 23 TYR A 81 GLY A 82 GLU A 99 ILE A 101 SITE 2 AC1 23 ARG A 106 ILE A 109 SER A 111 PRO A 113 SITE 3 AC1 23 GLU A 114 GLY A 115 ARG A 116 GLY A 117 SITE 4 AC1 23 VAL A 118 SER A 140 VAL A 141 GLY A 142 SITE 5 AC1 23 PHE A 143 PRO A 144 HIS A 147 MET A 150 SITE 6 AC1 23 PHE A 153 TYR A 169 HOH A2024 SITE 1 AC2 23 GLY B 82 PHE B 96 GLU B 99 ARG B 106 SITE 2 AC2 23 ILE B 109 GLY B 110 SER B 111 PRO B 113 SITE 3 AC2 23 GLU B 114 GLY B 115 ARG B 116 GLY B 117 SITE 4 AC2 23 VAL B 118 LEU B 119 SER B 140 VAL B 141 SITE 5 AC2 23 GLY B 142 PHE B 143 PRO B 144 HIS B 147 SITE 6 AC2 23 TYR B 169 THR B 171 OXY B1210 SITE 1 AC3 4 PRO B 113 LEU B 119 TYR B 169 HEM B1209 SITE 1 AC4 4 ARG A 87 ARG A 92 LEU A 93 PRO A 113 SITE 1 AC5 4 ARG B 87 ARG B 92 LEU B 93 PRO B 113 CRYST1 87.924 87.924 66.760 90.00 90.00 90.00 P 43 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 0.011373 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011373 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014979 0.00000