HEADER OXIDOREDUCTASE 07-DEC-25 9TJO TITLE CRYSTAL STRUCTURE OF THE APO CYP123 FROM MYCOBACTERIUM SMEGMATIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: STEROID C26-MONOOXYGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CHOLEST-4-EN-3-ONE C26-MONOOXYGENASE,CHOLESTEROL C26- COMPND 5 MONOOXYGENASE,STEROID C27-MONOOXYGENASE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 GENE: CYP123, MSMEI_5702; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A-CYP123 KEYWDS CYTOCHROME P450, MONOOXYGENASE, STEROL METABOLISM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.DONGXU,J.YI,Z.REMI,R.HANNAH REVDAT 1 04-NOV-26 9TJO 0 JRNL AUTH Y.DONGXU,H.LAUREN,R.HANNAH,Z.REMI,J.YI JRNL TITL FUNCTIONAL CHARACTERISATION OF MYCOBACTERIUM CYP123 IN THE JRNL TITL 2 HYDROXYLATION OF METHYL GROUPS AT THE C-4 POSITION IN JRNL TITL 3 STEROLS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 (REFMACAT 0.4.105) REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 62498 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.183 REMARK 3 FREE R VALUE TEST SET COUNT : 3239 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) : 2.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4307 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3530 REMARK 3 BIN FREE R VALUE SET COUNT : 236 REMARK 3 BIN FREE R VALUE : 0.3800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6289 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 99 REMARK 3 SOLVENT ATOMS : 186 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14200 REMARK 3 B22 (A**2) : -0.14200 REMARK 3 B33 (A**2) : 0.28500 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): 0.214 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.176 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.298 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6535 ; 0.004 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 6048 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8887 ; 1.251 ; 1.860 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13871 ; 0.444 ; 1.773 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 791 ; 6.700 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ; 6.858 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1060 ;14.234 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 966 ; 0.058 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7945 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1555 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1476 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 28 ; 0.156 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3183 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 251 ; 0.183 ; 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): 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): 3170 ; 3.371 ; 5.882 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3170 ; 3.370 ; 5.882 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3959 ; 4.944 ;10.569 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3960 ; 4.944 ;10.570 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3365 ; 3.472 ; 6.075 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3364 ; 3.472 ; 6.075 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4928 ; 5.282 ;11.062 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4929 ; 5.281 ;11.061 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 BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9TJO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1292151088. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62580 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 REMARK 200 RESOLUTION RANGE LOW (A) : 66.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 27.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 CITRATE TRIBASIC PH 5.6, 30% PEG 4000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 63.41750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 66.15700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 66.15700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 95.12625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 66.15700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 66.15700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.70875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 66.15700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 66.15700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 95.12625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 66.15700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 66.15700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.70875 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 63.41750 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 GLU B 402 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 160 OE2 GLU A 188 2.07 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 B 317 NE - CZ - NH2 ANGL. DEV. = -3.5 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 ALA A 32 55.84 -149.62 REMARK 500 ASN A 41 59.83 73.14 REMARK 500 SER A 46 -38.15 -132.72 REMARK 500 SER A 83 -143.54 58.48 REMARK 500 ALA A 86 42.56 -104.98 REMARK 500 VAL A 135 -75.17 -77.18 REMARK 500 PHE A 138 -75.14 -147.43 REMARK 500 ASN A 239 -77.15 -88.04 REMARK 500 ASP A 281 88.05 -152.89 REMARK 500 ASP A 294 153.29 -49.43 REMARK 500 ALA B 32 60.06 -167.75 REMARK 500 SER B 83 -139.85 56.71 REMARK 500 ALA B 86 42.49 -105.21 REMARK 500 PHE B 138 -82.18 -146.80 REMARK 500 GLU B 172 141.72 -37.78 REMARK 500 ASN B 239 -69.30 -95.53 REMARK 500 HIS B 267 3.29 -67.67 REMARK 500 ARG B 332 140.76 -33.39 REMARK 500 PHE B 347 135.58 -36.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 56 0.09 SIDE CHAIN REMARK 500 ARG A 317 0.09 SIDE CHAIN REMARK 500 ARG A 388 0.08 SIDE CHAIN REMARK 500 ARG B 56 0.09 SIDE CHAIN REMARK 500 ARG B 94 0.08 SIDE CHAIN REMARK 500 ARG B 317 0.10 SIDE CHAIN 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 CYS A 348 SG REMARK 620 2 HEM A 501 NA 95.6 REMARK 620 3 HEM A 501 NB 82.6 90.2 REMARK 620 4 HEM A 501 NC 88.7 173.6 85.7 REMARK 620 5 HEM A 501 ND 104.5 90.8 172.7 92.7 REMARK 620 6 HOH A 642 O 166.9 96.5 92.4 78.8 80.3 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 CYS B 348 SG REMARK 620 2 HEM B 501 NA 103.6 REMARK 620 3 HEM B 501 NB 92.0 88.4 REMARK 620 4 HEM B 501 NC 84.4 171.8 90.0 REMARK 620 5 HEM B 501 ND 94.3 88.9 173.6 91.8 REMARK 620 6 HOH B 608 O 174.2 70.7 88.6 101.3 85.0 REMARK 620 N 1 2 3 4 5 DBREF 9TJO A 6 400 UNP I7G922 I7G922_MYCS2 6 400 DBREF 9TJO B 6 400 UNP I7G922 I7G922_MYCS2 6 400 SEQADV 9TJO LEU A 401 UNP I7G922 EXPRESSION TAG SEQADV 9TJO GLU A 402 UNP I7G922 EXPRESSION TAG SEQADV 9TJO LEU B 401 UNP I7G922 EXPRESSION TAG SEQADV 9TJO GLU B 402 UNP I7G922 EXPRESSION TAG SEQRES 1 A 397 VAL GLU PRO VAL LEU ASP PRO TYR ASP TYR ASP PHE HIS SEQRES 2 A 397 GLU ASP PRO TYR PRO TYR TYR LYS ARG LEU ARG ASP GLU SEQRES 3 A 397 ALA PRO LEU TYR ARG ASN ASP GLU ARG ASN PHE TRP ALA SEQRES 4 A 397 LEU SER ARG HIS GLU ASP VAL LEU LYS GLY PHE ARG ASN SEQRES 5 A 397 SER THR ALA LEU SER ASN LYS HIS GLY VAL SER LEU ASP SEQRES 6 A 397 PRO VAL SER ARG ASN ASP GLU ALA HIS ARG VAL MET SER SEQRES 7 A 397 PHE LEU ALA LEU ASP ASP PRO ALA HIS LEU ARG LEU ARG SEQRES 8 A 397 THR LEU VAL SER LYS GLY PHE THR PRO ARG ARG ILE ARG SEQRES 9 A 397 GLU LEU GLU ALA ARG VAL THR GLU ILE ALA VAL GLN HIS SEQRES 10 A 397 LEU GLU ILE ALA LEU GLN SER ASP SER PHE ASP PHE VAL SEQRES 11 A 397 ASP ASP PHE ALA GLY LYS LEU PRO MET ASP VAL ILE SER SEQRES 12 A 397 GLU LEU MET GLY VAL PRO GLU GLU ASP ARG VAL ARG ILE SEQRES 13 A 397 ARG ALA LEU ALA ASP GLY VAL MET HIS ARG GLU ASP GLY SEQRES 14 A 397 VAL ALA ASP VAL PRO ALA SER ALA ILE ALA ALA SER GLY SEQRES 15 A 397 GLU LEU LEU VAL TYR TYR ALA ASP MET VAL LYS ARG ARG SEQRES 16 A 397 ARG ARG ASN VAL SER ASP ASP LEU THR SER ALA LEU VAL SEQRES 17 A 397 GLU ALA GLU ILE ASP GLY ASP LYS LEU THR ASP ASP GLU SEQRES 18 A 397 ILE MET ALA PHE LEU PHE LEU MET VAL VAL ALA GLY ASN SEQRES 19 A 397 GLU THR THR THR LYS LEU LEU ALA ASN ALA ALA TYR TRP SEQRES 20 A 397 GLY PHE LYS ASN PRO ASP GLN LEU ALA PRO VAL PHE ASP SEQRES 21 A 397 ASP HIS SER GLN ILE PRO LEU TRP VAL GLU GLU THR LEU SEQRES 22 A 397 ARG TYR ASP THR SER SER GLN ILE LEU ALA ARG ALA VAL SEQRES 23 A 397 VAL GLU ASP LEU THR PHE TYR GLY THR THR VAL PRO ALA SEQRES 24 A 397 GLY ASP VAL LEU VAL LEU LEU ALA GLY SER ALA ASN ARG SEQRES 25 A 397 ASP GLU ARG ALA PHE ASP ASP PRO ASP GLU TYR ARG ILE SEQRES 26 A 397 GLY ARG ASP ILE GLY SER LYS LEU VAL SER PHE GLY SER SEQRES 27 A 397 GLY ALA HIS PHE CYS LEU GLY ALA HIS LEU ALA ARG MET SEQRES 28 A 397 GLU ALA ARG VAL ALA LEU ALA GLU LEU PHE LYS ARG ILE SEQRES 29 A 397 ARG GLY TYR ASP VAL ASP GLU SER ALA SER VAL ARG VAL SEQRES 30 A 397 HIS SER SER SER VAL ARG GLY PHE ALA HIS LEU PRO ILE SEQRES 31 A 397 THR VAL GLU LYS ARG LEU GLU SEQRES 1 B 397 VAL GLU PRO VAL LEU ASP PRO TYR ASP TYR ASP PHE HIS SEQRES 2 B 397 GLU ASP PRO TYR PRO TYR TYR LYS ARG LEU ARG ASP GLU SEQRES 3 B 397 ALA PRO LEU TYR ARG ASN ASP GLU ARG ASN PHE TRP ALA SEQRES 4 B 397 LEU SER ARG HIS GLU ASP VAL LEU LYS GLY PHE ARG ASN SEQRES 5 B 397 SER THR ALA LEU SER ASN LYS HIS GLY VAL SER LEU ASP SEQRES 6 B 397 PRO VAL SER ARG ASN ASP GLU ALA HIS ARG VAL MET SER SEQRES 7 B 397 PHE LEU ALA LEU ASP ASP PRO ALA HIS LEU ARG LEU ARG SEQRES 8 B 397 THR LEU VAL SER LYS GLY PHE THR PRO ARG ARG ILE ARG SEQRES 9 B 397 GLU LEU GLU ALA ARG VAL THR GLU ILE ALA VAL GLN HIS SEQRES 10 B 397 LEU GLU ILE ALA LEU GLN SER ASP SER PHE ASP PHE VAL SEQRES 11 B 397 ASP ASP PHE ALA GLY LYS LEU PRO MET ASP VAL ILE SER SEQRES 12 B 397 GLU LEU MET GLY VAL PRO GLU GLU ASP ARG VAL ARG ILE SEQRES 13 B 397 ARG ALA LEU ALA ASP GLY VAL MET HIS ARG GLU ASP GLY SEQRES 14 B 397 VAL ALA ASP VAL PRO ALA SER ALA ILE ALA ALA SER GLY SEQRES 15 B 397 GLU LEU LEU VAL TYR TYR ALA ASP MET VAL LYS ARG ARG SEQRES 16 B 397 ARG ARG ASN VAL SER ASP ASP LEU THR SER ALA LEU VAL SEQRES 17 B 397 GLU ALA GLU ILE ASP GLY ASP LYS LEU THR ASP ASP GLU SEQRES 18 B 397 ILE MET ALA PHE LEU PHE LEU MET VAL VAL ALA GLY ASN SEQRES 19 B 397 GLU THR THR THR LYS LEU LEU ALA ASN ALA ALA TYR TRP SEQRES 20 B 397 GLY PHE LYS ASN PRO ASP GLN LEU ALA PRO VAL PHE ASP SEQRES 21 B 397 ASP HIS SER GLN ILE PRO LEU TRP VAL GLU GLU THR LEU SEQRES 22 B 397 ARG TYR ASP THR SER SER GLN ILE LEU ALA ARG ALA VAL SEQRES 23 B 397 VAL GLU ASP LEU THR PHE TYR GLY THR THR VAL PRO ALA SEQRES 24 B 397 GLY ASP VAL LEU VAL LEU LEU ALA GLY SER ALA ASN ARG SEQRES 25 B 397 ASP GLU ARG ALA PHE ASP ASP PRO ASP GLU TYR ARG ILE SEQRES 26 B 397 GLY ARG ASP ILE GLY SER LYS LEU VAL SER PHE GLY SER SEQRES 27 B 397 GLY ALA HIS PHE CYS LEU GLY ALA HIS LEU ALA ARG MET SEQRES 28 B 397 GLU ALA ARG VAL ALA LEU ALA GLU LEU PHE LYS ARG ILE SEQRES 29 B 397 ARG GLY TYR ASP VAL ASP GLU SER ALA SER VAL ARG VAL SEQRES 30 B 397 HIS SER SER SER VAL ARG GLY PHE ALA HIS LEU PRO ILE SEQRES 31 B 397 THR VAL GLU LYS ARG LEU GLU HET HEM A 501 43 HET CIT A 502 13 HET HEM B 501 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CIT CITRIC ACID HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 CIT C6 H8 O7 FORMUL 6 HOH *186(H2 O) HELIX 1 AA1 ASP A 14 ASP A 20 1 7 HELIX 2 AA2 PRO A 21 ALA A 32 1 12 HELIX 3 AA3 ARG A 47 ASN A 57 1 11 HELIX 4 AA4 ALA A 78 SER A 83 1 6 HELIX 5 AA5 PHE A 84 LEU A 87 5 4 HELIX 6 AA6 PRO A 90 LYS A 101 1 12 HELIX 7 AA7 THR A 104 LEU A 111 1 8 HELIX 8 AA8 LEU A 111 LEU A 127 1 17 HELIX 9 AA9 LYS A 141 GLY A 152 1 12 HELIX 10 AB1 PRO A 154 GLU A 156 5 3 HELIX 11 AB2 ASP A 157 ASP A 166 1 10 HELIX 12 AB3 GLY A 167 MET A 169 5 3 HELIX 13 AB4 ASP A 177 ASN A 203 1 27 HELIX 14 AB5 ASP A 207 ALA A 215 1 9 HELIX 15 AB6 THR A 223 ASN A 239 1 17 HELIX 16 AB7 ASN A 239 LYS A 255 1 17 HELIX 17 AB8 ASN A 256 ASP A 266 1 11 HELIX 18 AB9 GLN A 269 ASP A 281 1 13 HELIX 19 AC1 ALA A 312 ARG A 317 1 6 HELIX 20 AC2 SER A 343 PHE A 347 5 5 HELIX 21 AC3 GLY A 350 LYS A 367 1 18 HELIX 22 AC4 GLU A 376 SER A 379 5 4 HELIX 23 AC5 ASP B 14 ASP B 20 1 7 HELIX 24 AC6 PRO B 21 ALA B 32 1 12 HELIX 25 AC7 ARG B 47 ASN B 57 1 11 HELIX 26 AC8 ASP B 70 ARG B 74 5 5 HELIX 27 AC9 GLU B 77 SER B 83 1 7 HELIX 28 AD1 PHE B 84 LEU B 87 5 4 HELIX 29 AD2 PRO B 90 PHE B 103 1 14 HELIX 30 AD3 THR B 104 LEU B 127 1 24 HELIX 31 AD4 LYS B 141 GLY B 152 1 12 HELIX 32 AD5 ASP B 157 ASP B 166 1 10 HELIX 33 AD6 PRO B 179 ASN B 203 1 25 HELIX 34 AD7 ASP B 207 ALA B 215 1 9 HELIX 35 AD8 THR B 223 ASN B 239 1 17 HELIX 36 AD9 ASN B 239 ASN B 256 1 18 HELIX 37 AE1 ASN B 256 ASP B 266 1 11 HELIX 38 AE2 GLN B 269 ASP B 281 1 13 HELIX 39 AE3 ALA B 312 ARG B 317 1 6 HELIX 40 AE4 GLY B 350 ARG B 368 1 19 SHEET 1 AA1 5 LEU A 34 ASN A 37 0 SHEET 2 AA1 5 PHE A 42 LEU A 45 -1 O ALA A 44 N TYR A 35 SHEET 3 AA1 5 VAL A 307 LEU A 311 1 O VAL A 307 N TRP A 43 SHEET 4 AA1 5 ILE A 286 VAL A 291 -1 N LEU A 287 O LEU A 310 SHEET 5 AA1 5 LEU A 61 SER A 62 -1 N SER A 62 O ALA A 290 SHEET 1 AA2 3 SER A 131 ASP A 133 0 SHEET 2 AA2 3 PRO A 394 LYS A 399 -1 O ILE A 395 N PHE A 132 SHEET 3 AA2 3 ILE A 369 VAL A 374 -1 N ARG A 370 O GLU A 398 SHEET 1 AA3 2 LEU A 295 PHE A 297 0 SHEET 2 AA3 2 THR A 300 VAL A 302 -1 O THR A 300 N PHE A 297 SHEET 1 AA4 2 VAL A 380 ARG A 381 0 SHEET 2 AA4 2 PHE A 390 HIS A 392 -1 O ALA A 391 N VAL A 380 SHEET 1 AA5 5 LEU B 34 ASN B 37 0 SHEET 2 AA5 5 PHE B 42 LEU B 45 -1 O PHE B 42 N ASN B 37 SHEET 3 AA5 5 VAL B 307 LEU B 311 1 O VAL B 309 N TRP B 43 SHEET 4 AA5 5 ILE B 286 VAL B 291 -1 N LEU B 287 O LEU B 310 SHEET 5 AA5 5 LEU B 61 SER B 62 -1 N SER B 62 O ALA B 290 SHEET 1 AA6 3 SER B 131 ASP B 133 0 SHEET 2 AA6 3 PRO B 394 LYS B 399 -1 O ILE B 395 N PHE B 132 SHEET 3 AA6 3 ILE B 369 VAL B 374 -1 N ARG B 370 O GLU B 398 SHEET 1 AA7 2 LEU B 295 PHE B 297 0 SHEET 2 AA7 2 THR B 300 VAL B 302 -1 O VAL B 302 N LEU B 295 SHEET 1 AA8 2 VAL B 380 ARG B 381 0 SHEET 2 AA8 2 PHE B 390 HIS B 392 -1 O HIS B 392 N VAL B 380 LINK SG CYS A 348 FE HEM A 501 1555 1555 2.25 LINK FE HEM A 501 O HOH A 642 1555 1555 2.27 LINK SG CYS B 348 FE HEM B 501 1555 1555 2.31 LINK FE HEM B 501 O HOH B 608 1555 1555 2.27 CISPEP 1 ASP A 89 PRO A 90 0 5.24 CISPEP 2 ASP B 89 PRO B 90 0 7.79 CISPEP 3 VAL B 178 PRO B 179 0 -1.55 CRYST1 132.314 132.314 126.835 90.00 90.00 90.00 P 43 21 2 16 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 0.007558 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007558 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007884 0.00000 CONECT 2724 6334 CONECT 5874 6390 CONECT 6292 6296 6323 CONECT 6293 6299 6306 CONECT 6294 6309 6313 CONECT 6295 6316 6320 CONECT 6296 6292 6297 6330 CONECT 6297 6296 6298 6301 CONECT 6298 6297 6299 6300 CONECT 6299 6293 6298 6330 CONECT 6300 6298 CONECT 6301 6297 6302 CONECT 6302 6301 6303 CONECT 6303 6302 6304 6305 CONECT 6304 6303 CONECT 6305 6303 CONECT 6306 6293 6307 6331 CONECT 6307 6306 6308 6310 CONECT 6308 6307 6309 6311 CONECT 6309 6294 6308 6331 CONECT 6310 6307 CONECT 6311 6308 6312 CONECT 6312 6311 CONECT 6313 6294 6314 6332 CONECT 6314 6313 6315 6317 CONECT 6315 6314 6316 6318 CONECT 6316 6295 6315 6332 CONECT 6317 6314 CONECT 6318 6315 6319 CONECT 6319 6318 CONECT 6320 6295 6321 6333 CONECT 6321 6320 6322 6324 CONECT 6322 6321 6323 6325 CONECT 6323 6292 6322 6333 CONECT 6324 6321 CONECT 6325 6322 6326 CONECT 6326 6325 6327 CONECT 6327 6326 6328 6329 CONECT 6328 6327 CONECT 6329 6327 CONECT 6330 6296 6299 6334 CONECT 6331 6306 6309 6334 CONECT 6332 6313 6316 6334 CONECT 6333 6320 6323 6334 CONECT 6334 2724 6330 6331 6332 CONECT 6334 6333 6432 CONECT 6335 6336 6337 6338 CONECT 6336 6335 CONECT 6337 6335 CONECT 6338 6335 6339 CONECT 6339 6338 6340 6341 6345 CONECT 6340 6339 CONECT 6341 6339 6342 CONECT 6342 6341 6343 6344 CONECT 6343 6342 CONECT 6344 6342 CONECT 6345 6339 6346 6347 CONECT 6346 6345 CONECT 6347 6345 CONECT 6348 6352 6379 CONECT 6349 6355 6362 CONECT 6350 6365 6369 CONECT 6351 6372 6376 CONECT 6352 6348 6353 6386 CONECT 6353 6352 6354 6357 CONECT 6354 6353 6355 6356 CONECT 6355 6349 6354 6386 CONECT 6356 6354 CONECT 6357 6353 6358 CONECT 6358 6357 6359 CONECT 6359 6358 6360 6361 CONECT 6360 6359 CONECT 6361 6359 CONECT 6362 6349 6363 6387 CONECT 6363 6362 6364 6366 CONECT 6364 6363 6365 6367 CONECT 6365 6350 6364 6387 CONECT 6366 6363 CONECT 6367 6364 6368 CONECT 6368 6367 CONECT 6369 6350 6370 6388 CONECT 6370 6369 6371 6373 CONECT 6371 6370 6372 6374 CONECT 6372 6351 6371 6388 CONECT 6373 6370 CONECT 6374 6371 6375 CONECT 6375 6374 CONECT 6376 6351 6377 6389 CONECT 6377 6376 6378 6380 CONECT 6378 6377 6379 6381 CONECT 6379 6348 6378 6389 CONECT 6380 6377 CONECT 6381 6378 6382 CONECT 6382 6381 6383 CONECT 6383 6382 6384 6385 CONECT 6384 6383 CONECT 6385 6383 CONECT 6386 6352 6355 6390 CONECT 6387 6362 6365 6390 CONECT 6388 6369 6372 6390 CONECT 6389 6376 6379 6390 CONECT 6390 5874 6386 6387 6388 CONECT 6390 6389 6506 CONECT 6432 6334 CONECT 6506 6390 MASTER 377 0 3 40 24 0 0 6 6574 2 105 62 END