HEADER OXIDOREDUCTASE 09-APR-12 4APY TITLE ETHYLENE GLYCOL-BOUND FORM OF P450 CYP125A3 FROM MYCOBACTERIUM TITLE 2 SMEGMATIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: P450 HEME-THIOLATE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYP125A3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS STR. MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI DH5[ALPHA]; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 668369; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PCW KEYWDS OXIDOREDUCTASE, CHOLESTEROL METABOLISM EXPDTA X-RAY DIFFRACTION AUTHOR D.J.FRANK,E.GARCIA FERNANDEZ,P.M.KELLS,J.L.GARCIA LOPEZ,L.M.PODUST, AUTHOR 2 P.R.ORTIZ DE MONTELLANO REVDAT 5 20-DEC-23 4APY 1 REMARK LINK REVDAT 4 07-FEB-18 4APY 1 SOURCE JRNL REVDAT 3 14-AUG-13 4APY 1 JRNL REVDAT 2 01-MAY-13 4APY 1 JRNL REVDAT 1 27-FEB-13 4APY 0 JRNL AUTH E.GARCIA-FERNANDEZ,D.J.FRANK,B.GALAN,P.M.KELLS,L.M.PODUST, JRNL AUTH 2 J.L.GARCIA,P.R.ORTIZ DE MONTELLANO JRNL TITL A HIGHLY CONSERVED MYCOBACTERIAL CHOLESTEROL CATABOLIC JRNL TITL 2 PATHWAY. JRNL REF ENVIRON.MICROBIOL. V. 15 2342 2013 JRNL REFN ISSN 1462-2912 JRNL PMID 23489718 JRNL DOI 10.1111/1462-2920.12108 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 76.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 43952 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2341 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) : 3176 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.3070 REMARK 3 BIN FREE R VALUE SET COUNT : 172 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3212 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 339 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.31000 REMARK 3 B22 (A**2) : 0.31000 REMARK 3 B33 (A**2) : -0.61000 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): 0.119 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.364 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3421 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4645 ; 2.056 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 425 ; 6.270 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;36.451 ;24.472 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 546 ;14.521 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;14.938 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 491 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2654 ; 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): 2099 ; 1.200 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3384 ; 2.138 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1322 ; 3.441 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1261 ; 5.248 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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. REMARK 4 REMARK 4 4APY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-APR-12. REMARK 100 THE DEPOSITION ID IS D_1290052025. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.5 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 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46604 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 80.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3000 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.85000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2X5W REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 45% TACSIMATE, PH 7.0; 2% GLUCOSE; 0.1 REMARK 280 M NA CACODYLATE, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,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 54.09400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 54.09400 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.11700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 54.09400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.05850 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 54.09400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.17550 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 54.09400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.09400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 60.11700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 54.09400 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 90.17550 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 54.09400 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 30.05850 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: 9080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.2 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 108.18800 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 1 REMARK 465 VAL A 416 REMARK 465 SER A 417 REMARK 465 GLY A 418 REMARK 465 ALA A 419 REMARK 465 PRO A 420 REMARK 465 GLY A 421 REMARK 465 THR A 422 REMARK 465 CYS A 423 REMARK 465 PRO A 424 REMARK 465 VAL A 425 REMARK 465 ALA A 426 REMARK 465 HIS A 427 REMARK 465 HIS A 428 REMARK 465 HIS A 429 REMARK 465 HIS A 430 REMARK 465 HIS A 431 REMARK 465 HIS A 432 REMARK 465 HIS A 433 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 ARG A 121 CZ NH1 NH2 REMARK 470 GLU A 151 OE1 OE2 REMARK 470 GLU A 220 CG CD OE1 OE2 REMARK 470 GLU A 228 CD OE1 OE2 REMARK 470 ILE A 231 CG1 CG2 CD1 REMARK 470 LYS A 385 CD CE NZ REMARK 470 LYS A 413 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 O1A HEM A 1418 O HOH A 2277 1.91 REMARK 500 OE1 GLU A 391 O HOH A 2327 2.07 REMARK 500 O HOH A 2047 O HOH A 2146 2.13 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 PHE A 201 CB PHE A 201 CG 0.103 REMARK 500 TYR A 324 CD1 TYR A 324 CE1 0.100 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 68 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 89 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 178 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A 239 CB - CG - OD1 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG A 291 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP A 306 CB - CG - OD1 ANGL. DEV. = 5.4 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 GLU A 34 76.90 -160.70 REMARK 500 ARG A 68 55.37 -95.06 REMARK 500 ALA A 185 -38.64 -37.56 REMARK 500 ASN A 253 -81.80 -109.02 REMARK 500 THR A 294 66.25 27.38 REMARK 500 MET A 381 49.84 -154.51 REMARK 500 TRP A 397 -21.74 -142.27 REMARK 500 ALA A 411 35.12 -151.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2068 DISTANCE = 6.51 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 1,2-ETHANEDIOL (EDO): CRYO-PROTECTANT AGENT REMARK 600 PROTOPORPHYRIN IX CONTAINING FE (HEM): HEME THIOLATE BOND TO REMARK 600 CYS 360 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 A1418 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 360 SG REMARK 620 2 HEM A1418 NA 98.0 REMARK 620 3 HEM A1418 NB 90.2 86.3 REMARK 620 4 HEM A1418 NC 86.3 175.6 94.4 REMARK 620 5 HEM A1418 ND 94.6 92.5 175.3 86.5 REMARK 620 6 EDO A1423 O2 176.3 84.4 87.2 91.3 88.1 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 EDO A 1416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 1418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1420 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1421 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1422 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1423 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1424 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1425 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1427 REMARK 999 REMARK 999 SEQUENCE REMARK 999 6XHIS TAG IS ENGINEERED AT C-TERMINUS DBREF 4APY A 1 427 UNP A0R4Y3 A0R4Y3_MYCS2 1 427 SEQADV 4APY HIS A 428 UNP A0R4Y3 EXPRESSION TAG SEQADV 4APY HIS A 429 UNP A0R4Y3 EXPRESSION TAG SEQADV 4APY HIS A 430 UNP A0R4Y3 EXPRESSION TAG SEQADV 4APY HIS A 431 UNP A0R4Y3 EXPRESSION TAG SEQADV 4APY HIS A 432 UNP A0R4Y3 EXPRESSION TAG SEQADV 4APY HIS A 433 UNP A0R4Y3 EXPRESSION TAG SEQRES 1 A 433 MET PRO THR PRO ASN ILE PRO SER ASP PHE ASP PHE LEU SEQRES 2 A 433 ASP ALA THR LEU ASN LEU GLU ARG LEU PRO VAL GLU GLU SEQRES 3 A 433 LEU ALA GLU LEU ARG LYS SER GLU PRO ILE HIS TRP VAL SEQRES 4 A 433 ASP VAL PRO GLY GLY THR GLY GLY PHE GLY ASP LYS GLY SEQRES 5 A 433 TYR TRP LEU VAL THR LYS HIS ALA ASP VAL LYS GLU VAL SEQRES 6 A 433 SER ARG ARG SER ASP VAL PHE GLY SER SER PRO ASP GLY SEQRES 7 A 433 ALA ILE PRO VAL TRP PRO GLN ASP MET THR ARG GLU ALA SEQRES 8 A 433 VAL ASP LEU GLN ARG ALA VAL LEU LEU ASN MET ASP ALA SEQRES 9 A 433 PRO GLN HIS THR ARG LEU ARG LYS ILE ILE SER ARG GLY SEQRES 10 A 433 PHE THR PRO ARG ALA ILE GLY ARG LEU GLU ASP GLU LEU SEQRES 11 A 433 ARG SER ARG ALA GLN LYS ILE ALA GLN THR ALA ALA ALA SEQRES 12 A 433 GLN GLY ALA GLY ASP PHE VAL GLU GLN VAL SER CYS GLU SEQRES 13 A 433 LEU PRO LEU GLN ALA ILE ALA GLU LEU LEU GLY VAL PRO SEQRES 14 A 433 GLN ASP ASP ARG ASP LYS LEU PHE ARG TRP SER ASN GLU SEQRES 15 A 433 MET THR ALA GLY GLU ASP PRO GLU TYR ALA ASP VAL ASP SEQRES 16 A 433 PRO ALA MET SER SER PHE GLU LEU ILE SER TYR ALA MET SEQRES 17 A 433 LYS MET ALA GLU GLU ARG ALA VAL ASN PRO THR GLU ASP SEQRES 18 A 433 ILE VAL THR LYS LEU ILE GLU ALA ASP ILE ASP GLY GLU SEQRES 19 A 433 LYS LEU SER ASP ASP GLU PHE GLY PHE PHE VAL VAL MET SEQRES 20 A 433 LEU ALA VAL ALA GLY ASN GLU THR THR ARG ASN SER ILE SEQRES 21 A 433 THR HIS GLY MET ILE ALA PHE ALA GLN ASN PRO ASP GLN SEQRES 22 A 433 TRP GLU LEU TYR LYS LYS GLU ARG PRO GLU THR ALA ALA SEQRES 23 A 433 ASP GLU ILE VAL ARG TRP ALA THR PRO VAL SER ALA PHE SEQRES 24 A 433 GLN ARG THR ALA LEU GLU ASP VAL GLU LEU GLY GLY VAL SEQRES 25 A 433 GLN ILE LYS LYS GLY GLN ARG VAL VAL MET SER TYR ARG SEQRES 26 A 433 SER ALA ASN PHE ASP GLU GLU VAL PHE GLU ASP PRO HIS SEQRES 27 A 433 THR PHE ASN ILE LEU ARG SER PRO ASN PRO HIS VAL GLY SEQRES 28 A 433 PHE GLY GLY THR GLY ALA HIS TYR CYS ILE GLY ALA ASN SEQRES 29 A 433 LEU ALA ARG MET THR ILE ASN LEU ILE PHE ASN ALA ILE SEQRES 30 A 433 ALA ASP ASN MET PRO ASP LEU LYS PRO ILE GLY ALA PRO SEQRES 31 A 433 GLU ARG LEU LYS SER GLY TRP LEU ASN GLY ILE LYS HIS SEQRES 32 A 433 TRP GLN VAL ASP TYR THR GLY ALA GLY LYS ALA SER VAL SEQRES 33 A 433 SER GLY ALA PRO GLY THR CYS PRO VAL ALA HIS HIS HIS SEQRES 34 A 433 HIS HIS HIS HIS HET EDO A1416 4 HET EDO A1417 4 HET HEM A1418 43 HET EDO A1419 4 HET EDO A1420 4 HET EDO A1421 4 HET EDO A1422 4 HET EDO A1423 4 HET EDO A1424 4 HET EDO A1425 4 HET CL A1426 1 HET EDO A1427 4 HET EDO A1428 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL HETSYN HEM HEME FORMUL 2 EDO 11(C2 H6 O2) FORMUL 4 HEM C34 H32 FE N4 O4 FORMUL 12 CL CL 1- FORMUL 15 HOH *339(H2 O) HELIX 1 1 ASP A 14 ARG A 21 1 8 HELIX 2 2 PRO A 23 GLU A 34 1 12 HELIX 3 3 LYS A 58 ARG A 68 1 11 HELIX 4 4 THR A 88 LEU A 94 1 7 HELIX 5 5 GLN A 95 MET A 102 5 8 HELIX 6 6 PRO A 105 SER A 115 1 11 HELIX 7 7 ARG A 116 PHE A 118 5 3 HELIX 8 8 THR A 119 ARG A 125 1 7 HELIX 9 9 LEU A 126 ALA A 143 1 18 HELIX 10 10 PHE A 149 VAL A 153 1 5 HELIX 11 11 CYS A 155 GLY A 167 1 13 HELIX 12 12 PRO A 169 ASP A 171 5 3 HELIX 13 13 ASP A 172 THR A 184 1 13 HELIX 14 14 ASP A 188 ALA A 192 5 5 HELIX 15 15 ASP A 195 ASN A 217 1 23 HELIX 16 16 ASP A 221 GLU A 228 1 8 HELIX 17 17 SER A 237 GLY A 252 1 16 HELIX 18 18 ASN A 253 ASN A 270 1 18 HELIX 19 19 ASN A 270 ARG A 281 1 12 HELIX 20 20 THR A 284 THR A 294 1 11 HELIX 21 21 TYR A 324 ASN A 328 1 5 HELIX 22 22 GLY A 362 MET A 381 1 20 SHEET 1 AA 5 ILE A 36 ASP A 40 0 SHEET 2 AA 5 GLY A 52 VAL A 56 -1 O TYR A 53 N VAL A 39 SHEET 3 AA 5 ARG A 319 SER A 323 1 O ARG A 319 N TRP A 54 SHEET 4 AA 5 ALA A 298 ALA A 303 -1 O PHE A 299 N MET A 322 SHEET 5 AA 5 PHE A 72 GLY A 73 -1 O GLY A 73 N THR A 302 SHEET 1 AB 3 ALA A 146 ASP A 148 0 SHEET 2 AB 3 GLN A 405 ASP A 407 -1 O VAL A 406 N GLY A 147 SHEET 3 AB 3 LYS A 385 PRO A 386 -1 O LYS A 385 N ASP A 407 SHEET 1 AC 2 VAL A 307 LEU A 309 0 SHEET 2 AC 2 VAL A 312 ILE A 314 -1 O VAL A 312 N LEU A 309 SHEET 1 AD 2 GLU A 391 ARG A 392 0 SHEET 2 AD 2 ILE A 401 HIS A 403 -1 N LYS A 402 O GLU A 391 LINK SG CYS A 360 FE HEM A1418 1555 1555 2.38 LINK FE HEM A1418 O2 EDO A1423 1555 1555 2.33 CISPEP 1 ALA A 104 PRO A 105 0 4.38 CISPEP 2 SER A 345 PRO A 346 0 -0.29 SITE 1 AC1 6 GLU A 20 LYS A 63 PRO A 348 HIS A 349 SITE 2 AC1 6 THR A 355 HOH A2095 SITE 1 AC2 6 TYR A 277 ARG A 281 PRO A 282 GLU A 283 SITE 2 AC2 6 ASN A 371 ASN A 375 SITE 1 AC3 25 LEU A 99 LEU A 100 HIS A 107 ARG A 111 SITE 2 AC3 25 ALA A 251 GLY A 252 THR A 255 THR A 256 SITE 3 AC3 25 PRO A 295 PHE A 299 ARG A 301 TYR A 324 SITE 4 AC3 25 GLY A 351 PHE A 352 GLY A 353 GLY A 354 SITE 5 AC3 25 ALA A 357 HIS A 358 CYS A 360 ILE A 361 SITE 6 AC3 25 GLY A 362 EDO A1423 HOH A2105 HOH A2277 SITE 7 AC3 25 HOH A2314 SITE 1 AC4 3 HIS A 262 ARG A 392 HOH A2245 SITE 1 AC5 5 VAL A 24 TRP A 292 HIS A 338 HOH A2272 SITE 2 AC5 5 HOH A2296 SITE 1 AC6 4 ILE A 80 PHE A 299 EDO A1423 HOH A2135 SITE 1 AC7 5 SER A 75 PRO A 76 ASP A 93 ARG A 96 SITE 2 AC7 5 HOH A2134 SITE 1 AC8 4 MET A 247 ALA A 251 HEM A1418 EDO A1421 SITE 1 AC9 4 CYS A 155 GLU A 156 ASN A 181 HOH A2211 SITE 1 BC1 4 ASP A 195 PRO A 196 ALA A 197 MET A 198 SITE 1 BC2 4 PHE A 10 ASP A 11 ASP A 14 HOH A2030 CRYST1 108.188 108.188 120.234 90.00 90.00 90.00 I 41 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 0.009243 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009243 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008317 0.00000