HEADER ISOMERASE 12-JAN-24 8RP3 TITLE ALPHA-METHYLACYL-COA RACEMASE FROM MYCOBACTERIUM TUBERCULOSIS (H126A TITLE 2 MUTANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-METHYLACYL-COA RACEMASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: AMACR,MTMCR; COMPND 5 EC: 5.1.99.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: MCR, RV1143; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS COA-TRANSFERASE, EPIMERIZATION, COA-TRANSFERASE FAMILY III, ALPHA KEYWDS 2 PROTON EXCHANGE, HOMO DIMER, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR O.O.MOJANAGA,K.R.ACHARYA,M.D.LLOYD REVDAT 1 10-APR-24 8RP3 0 JRNL AUTH O.O.MOJANAGA,T.J.WOODMAN,M.D.LLOYD,K.R.ACHARYA JRNL TITL ALPHA-METHYLACYL-COA RACEMASE FROM MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS -DETAILED KINETIC AND STRUCTURAL JRNL TITL 3 CHARACTERIZATION OF THE ACTIVE SITE. JRNL REF BIOMOLECULES V. 14 2024 JRNL REFN ESSN 2218-273X JRNL PMID 38540719 JRNL DOI 10.3390/BIOM14030299 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 90.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 30847 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) : 0.188 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.759 REMARK 3 FREE R VALUE TEST SET COUNT : 1468 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) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2145 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.3470 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5356 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13600 REMARK 3 B22 (A**2) : -2.91200 REMARK 3 B33 (A**2) : 2.73200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.69000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.395 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.281 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.272 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.372 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.885 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5502 ; 0.015 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 5201 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7478 ; 2.645 ; 1.808 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11932 ; 0.850 ; 1.748 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 704 ; 7.955 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 52 ;10.575 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 850 ;16.325 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 811 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6756 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1280 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1233 ; 0.239 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 30 ; 0.270 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2694 ; 0.192 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 154 ; 0.160 ; 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): 2828 ; 7.006 ; 4.684 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2828 ; 6.994 ; 4.685 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3528 ; 9.515 ; 8.396 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3529 ; 9.516 ; 8.398 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2674 ; 7.828 ; 4.945 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2675 ; 7.826 ; 4.945 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3950 ;10.244 ; 8.926 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3951 ;10.242 ; 8.926 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 359 NULL REMARK 3 1 A 1 A 359 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT 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 8RP3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1292135821. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30851 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 90.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.36800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 8.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 90.52 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.05500 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 (%): 55.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.03 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.03 M CALCIUM CHLORIDE DIHYDRATE, 20 % (V/V) ETHYLENE GLYCOL, REMARK 280 10 % (W/V) PEG 8000, 0.1 M SODIUM (HEPES-MOPS), PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 90.55300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.57650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 90.55300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.57650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 13380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 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 MET A 0 REMARK 465 SER A 40 REMARK 465 SER A 41 REMARK 465 VAL A 42 REMARK 465 ASP A 43 REMARK 465 GLY A 44 REMARK 465 GLY A 360 REMARK 465 GLY A 361 REMARK 465 SER A 362 REMARK 465 GLY A 363 REMARK 465 CYS A 364 REMARK 465 MET B 0 REMARK 465 SER B 40 REMARK 465 SER B 41 REMARK 465 VAL B 42 REMARK 465 ASP B 43 REMARK 465 GLY B 44 REMARK 465 GLY B 360 REMARK 465 GLY B 361 REMARK 465 SER B 362 REMARK 465 GLY B 363 REMARK 465 CYS B 364 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 H ASP B 127 HO2 EDO B 401 1.28 REMARK 500 HG23 THR A 209 H THR A 211 1.28 REMARK 500 HD1 HIS A 312 H ARG B 120 1.34 REMARK 500 HH TYR B 223 HD21 ASN B 263 1.35 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 GLU B 12 CD GLU B 12 OE2 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 ARG A 35 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP A 48 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 48 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 54 CB - CA - C ANGL. DEV. = -12.5 DEGREES REMARK 500 ARG A 54 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 LYS A 62 CB - CA - C ANGL. DEV. = 17.2 DEGREES REMARK 500 LEU A 71 CB - CG - CD1 ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 146 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 203 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 203 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 MET A 207 CG - SD - CE ANGL. DEV. = -11.3 DEGREES REMARK 500 ARG A 212 NE - CZ - NH1 ANGL. DEV. = -6.2 DEGREES REMARK 500 MET A 216 CG - SD - CE ANGL. DEV. = 30.4 DEGREES REMARK 500 GLU A 241 CG - CD - OE1 ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG A 267 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 GLU A 270 CG - CD - OE2 ANGL. DEV. = -12.2 DEGREES REMARK 500 ARG A 284 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 284 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 GLU A 321 OE1 - CD - OE2 ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG A 333 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 GLU B 12 OE1 - CD - OE2 ANGL. DEV. = 10.3 DEGREES REMARK 500 ARG B 35 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 35 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ASP B 48 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG B 54 CB - CA - C ANGL. DEV. = -16.9 DEGREES REMARK 500 ARG B 54 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 120 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG B 120 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 GLN B 123 N - CA - CB ANGL. DEV. = -12.5 DEGREES REMARK 500 ARG B 203 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 MET B 207 CG - SD - CE ANGL. DEV. = -10.2 DEGREES REMARK 500 ARG B 212 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 MET B 216 CG - SD - CE ANGL. DEV. = -11.8 DEGREES REMARK 500 LEU B 252 CB - CG - CD1 ANGL. DEV. = -11.8 DEGREES REMARK 500 ARG B 265 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 333 NE - CZ - NH1 ANGL. DEV. = -3.9 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 14 126.26 -35.37 REMARK 500 LEU A 61 -5.66 -58.73 REMARK 500 ASN A 103 90.89 -168.12 REMARK 500 LEU A 151 -140.98 51.26 REMARK 500 PHE A 157 -76.22 -100.24 REMARK 500 ASP A 225 176.34 177.24 REMARK 500 ASP A 295 35.23 -87.70 REMARK 500 ALA A 346 126.01 79.06 REMARK 500 THR A 348 173.15 -56.97 REMARK 500 ALA B 14 120.66 -34.69 REMARK 500 ASN B 103 93.47 -167.34 REMARK 500 LEU B 151 -142.59 55.17 REMARK 500 PHE B 157 -81.92 -101.49 REMARK 500 SER B 177 -11.49 -148.86 REMARK 500 GLN B 182 172.86 171.84 REMARK 500 ASP B 210 -6.78 -58.94 REMARK 500 ASN B 323 -139.38 57.35 REMARK 500 THR B 337 77.71 -101.83 REMARK 500 THR B 348 170.46 -38.84 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 55 0.14 SIDE CHAIN REMARK 500 ARG A 105 0.08 SIDE CHAIN REMARK 500 ARG A 203 0.09 SIDE CHAIN REMARK 500 ARG A 212 0.20 SIDE CHAIN REMARK 500 ARG A 233 0.10 SIDE CHAIN REMARK 500 ARG A 265 0.07 SIDE CHAIN REMARK 500 ARG A 267 0.10 SIDE CHAIN REMARK 500 ARG B 105 0.11 SIDE CHAIN REMARK 500 ARG B 203 0.10 SIDE CHAIN REMARK 500 ARG B 212 0.14 SIDE CHAIN REMARK 500 ARG B 267 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8RP3 A 1 360 UNP O06543 AMACR_MYCTU 1 360 DBREF 8RP3 B 1 360 UNP O06543 AMACR_MYCTU 1 360 SEQADV 8RP3 MET A 0 UNP O06543 INITIATING METHIONINE SEQADV 8RP3 ALA A 126 UNP O06543 HIS 126 ENGINEERED MUTATION SEQADV 8RP3 GLY A 361 UNP O06543 EXPRESSION TAG SEQADV 8RP3 SER A 362 UNP O06543 EXPRESSION TAG SEQADV 8RP3 GLY A 363 UNP O06543 EXPRESSION TAG SEQADV 8RP3 CYS A 364 UNP O06543 EXPRESSION TAG SEQADV 8RP3 MET B 0 UNP O06543 INITIATING METHIONINE SEQADV 8RP3 ALA B 126 UNP O06543 HIS 126 ENGINEERED MUTATION SEQADV 8RP3 GLY B 361 UNP O06543 EXPRESSION TAG SEQADV 8RP3 SER B 362 UNP O06543 EXPRESSION TAG SEQADV 8RP3 GLY B 363 UNP O06543 EXPRESSION TAG SEQADV 8RP3 CYS B 364 UNP O06543 EXPRESSION TAG SEQRES 1 A 365 MET MET ALA GLY PRO LEU SER GLY LEU ARG VAL VAL GLU SEQRES 2 A 365 LEU ALA GLY ILE GLY PRO GLY PRO HIS ALA ALA MET ILE SEQRES 3 A 365 LEU GLY ASP LEU GLY ALA ASP VAL VAL ARG ILE ASP ARG SEQRES 4 A 365 PRO SER SER VAL ASP GLY ILE SER ARG ASP ALA MET LEU SEQRES 5 A 365 ARG ASN ARG ARG ILE VAL THR ALA ASP LEU LYS SER ASP SEQRES 6 A 365 GLN GLY LEU GLU LEU ALA LEU LYS LEU ILE ALA LYS ALA SEQRES 7 A 365 ASP VAL LEU ILE GLU GLY TYR ARG PRO GLY VAL THR GLU SEQRES 8 A 365 ARG LEU GLY LEU GLY PRO GLU GLU CYS ALA LYS VAL ASN SEQRES 9 A 365 ASP ARG LEU ILE TYR ALA ARG MET THR GLY TRP GLY GLN SEQRES 10 A 365 THR GLY PRO ARG SER GLN GLN ALA GLY ALA ASP ILE ASN SEQRES 11 A 365 TYR ILE SER LEU ASN GLY ILE LEU HIS ALA ILE GLY ARG SEQRES 12 A 365 GLY ASP GLU ARG PRO VAL PRO PRO LEU ASN LEU VAL GLY SEQRES 13 A 365 ASP PHE GLY GLY GLY SER MET PHE LEU LEU VAL GLY ILE SEQRES 14 A 365 LEU ALA ALA LEU TRP GLU ARG GLN SER SER GLY LYS GLY SEQRES 15 A 365 GLN VAL VAL ASP ALA ALA MET VAL ASP GLY SER SER VAL SEQRES 16 A 365 LEU ILE GLN MET MET TRP ALA MET ARG ALA THR GLY MET SEQRES 17 A 365 TRP THR ASP THR ARG GLY ALA ASN MET LEU ASP GLY GLY SEQRES 18 A 365 ALA PRO TYR TYR ASP THR TYR GLU CYS ALA ASP GLY ARG SEQRES 19 A 365 TYR VAL ALA VAL GLY ALA ILE GLU PRO GLN PHE TYR ALA SEQRES 20 A 365 ALA MET LEU ALA GLY LEU GLY LEU ASP ALA ALA GLU LEU SEQRES 21 A 365 PRO PRO GLN ASN ASP ARG ALA ARG TRP PRO GLU LEU ARG SEQRES 22 A 365 ALA LEU LEU THR GLU ALA PHE ALA SER HIS ASP ARG ASP SEQRES 23 A 365 HIS TRP GLY ALA VAL PHE ALA ASN SER ASP ALA CYS VAL SEQRES 24 A 365 THR PRO VAL LEU ALA PHE GLY GLU VAL HIS ASN GLU PRO SEQRES 25 A 365 HIS ILE ILE GLU ARG ASN THR PHE TYR GLU ALA ASN GLY SEQRES 26 A 365 GLY TRP GLN PRO MET PRO ALA PRO ARG PHE SER ARG THR SEQRES 27 A 365 ALA SER SER GLN PRO ARG PRO PRO ALA ALA THR ILE ASP SEQRES 28 A 365 ILE GLU ALA VAL LEU THR ASP TRP ASP GLY GLY SER GLY SEQRES 29 A 365 CYS SEQRES 1 B 365 MET MET ALA GLY PRO LEU SER GLY LEU ARG VAL VAL GLU SEQRES 2 B 365 LEU ALA GLY ILE GLY PRO GLY PRO HIS ALA ALA MET ILE SEQRES 3 B 365 LEU GLY ASP LEU GLY ALA ASP VAL VAL ARG ILE ASP ARG SEQRES 4 B 365 PRO SER SER VAL ASP GLY ILE SER ARG ASP ALA MET LEU SEQRES 5 B 365 ARG ASN ARG ARG ILE VAL THR ALA ASP LEU LYS SER ASP SEQRES 6 B 365 GLN GLY LEU GLU LEU ALA LEU LYS LEU ILE ALA LYS ALA SEQRES 7 B 365 ASP VAL LEU ILE GLU GLY TYR ARG PRO GLY VAL THR GLU SEQRES 8 B 365 ARG LEU GLY LEU GLY PRO GLU GLU CYS ALA LYS VAL ASN SEQRES 9 B 365 ASP ARG LEU ILE TYR ALA ARG MET THR GLY TRP GLY GLN SEQRES 10 B 365 THR GLY PRO ARG SER GLN GLN ALA GLY ALA ASP ILE ASN SEQRES 11 B 365 TYR ILE SER LEU ASN GLY ILE LEU HIS ALA ILE GLY ARG SEQRES 12 B 365 GLY ASP GLU ARG PRO VAL PRO PRO LEU ASN LEU VAL GLY SEQRES 13 B 365 ASP PHE GLY GLY GLY SER MET PHE LEU LEU VAL GLY ILE SEQRES 14 B 365 LEU ALA ALA LEU TRP GLU ARG GLN SER SER GLY LYS GLY SEQRES 15 B 365 GLN VAL VAL ASP ALA ALA MET VAL ASP GLY SER SER VAL SEQRES 16 B 365 LEU ILE GLN MET MET TRP ALA MET ARG ALA THR GLY MET SEQRES 17 B 365 TRP THR ASP THR ARG GLY ALA ASN MET LEU ASP GLY GLY SEQRES 18 B 365 ALA PRO TYR TYR ASP THR TYR GLU CYS ALA ASP GLY ARG SEQRES 19 B 365 TYR VAL ALA VAL GLY ALA ILE GLU PRO GLN PHE TYR ALA SEQRES 20 B 365 ALA MET LEU ALA GLY LEU GLY LEU ASP ALA ALA GLU LEU SEQRES 21 B 365 PRO PRO GLN ASN ASP ARG ALA ARG TRP PRO GLU LEU ARG SEQRES 22 B 365 ALA LEU LEU THR GLU ALA PHE ALA SER HIS ASP ARG ASP SEQRES 23 B 365 HIS TRP GLY ALA VAL PHE ALA ASN SER ASP ALA CYS VAL SEQRES 24 B 365 THR PRO VAL LEU ALA PHE GLY GLU VAL HIS ASN GLU PRO SEQRES 25 B 365 HIS ILE ILE GLU ARG ASN THR PHE TYR GLU ALA ASN GLY SEQRES 26 B 365 GLY TRP GLN PRO MET PRO ALA PRO ARG PHE SER ARG THR SEQRES 27 B 365 ALA SER SER GLN PRO ARG PRO PRO ALA ALA THR ILE ASP SEQRES 28 B 365 ILE GLU ALA VAL LEU THR ASP TRP ASP GLY GLY SER GLY SEQRES 29 B 365 CYS HET EDO A 401 10 HET EDO A 402 10 HET EDO B 401 10 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 3(C2 H6 O2) FORMUL 6 HOH *61(H2 O) HELIX 1 AA1 GLY A 17 LEU A 29 1 13 HELIX 2 AA2 SER A 63 ALA A 75 1 13 HELIX 3 AA3 GLY A 87 GLY A 93 1 7 HELIX 4 AA4 GLY A 95 ASN A 103 1 9 HELIX 5 AA5 ALA A 126 LEU A 133 1 8 HELIX 6 AA6 ILE A 136 ILE A 140 5 5 HELIX 7 AA7 GLY A 160 GLY A 179 1 20 HELIX 8 AA8 MET A 188 ILE A 196 1 9 HELIX 9 AA9 ILE A 196 ALA A 204 1 9 HELIX 10 AB1 GLU A 241 LEU A 252 1 12 HELIX 11 AB2 ASP A 255 LEU A 259 5 5 HELIX 12 AB3 ASP A 264 ALA A 266 5 3 HELIX 13 AB4 ARG A 267 SER A 281 1 15 HELIX 14 AB5 ASP A 283 PHE A 291 1 9 HELIX 15 AB6 ALA A 303 ASN A 309 5 7 HELIX 16 AB7 GLU A 310 ARG A 316 1 7 HELIX 17 AB8 ILE A 351 TRP A 358 1 8 HELIX 18 AB9 GLY B 17 LEU B 29 1 13 HELIX 19 AC1 ASP B 48 ARG B 52 5 5 HELIX 20 AC2 SER B 63 LYS B 76 1 14 HELIX 21 AC3 GLY B 87 LEU B 92 1 6 HELIX 22 AC4 GLY B 95 ASN B 103 1 9 HELIX 23 AC5 ALA B 126 LEU B 133 1 8 HELIX 24 AC6 ILE B 136 ILE B 140 5 5 HELIX 25 AC7 GLY B 160 GLY B 179 1 20 HELIX 26 AC8 MET B 188 ILE B 196 1 9 HELIX 27 AC9 ILE B 196 THR B 205 1 10 HELIX 28 AD1 GLU B 241 GLY B 253 1 13 HELIX 29 AD2 ASP B 255 LEU B 259 5 5 HELIX 30 AD3 ASP B 264 ALA B 266 5 3 HELIX 31 AD4 ARG B 267 SER B 281 1 15 HELIX 32 AD5 ASP B 283 PHE B 291 1 9 HELIX 33 AD6 ALA B 303 ASN B 309 5 7 HELIX 34 AD7 GLU B 310 ARG B 316 1 7 HELIX 35 AD8 ILE B 351 ASP B 359 1 9 SHEET 1 AA1 7 ARG A 55 THR A 58 0 SHEET 2 AA1 7 ASP A 32 ASP A 37 1 N ARG A 35 O VAL A 57 SHEET 3 AA1 7 ARG A 9 LEU A 13 1 N VAL A 10 O VAL A 34 SHEET 4 AA1 7 VAL A 79 GLU A 82 1 O VAL A 79 N VAL A 11 SHEET 5 AA1 7 ILE A 107 THR A 112 1 O ILE A 107 N LEU A 80 SHEET 6 AA1 7 VAL A 183 ALA A 187 1 O VAL A 184 N ARG A 110 SHEET 7 AA1 7 ARG B 333 PHE B 334 -1 O ARG B 333 N ASP A 185 SHEET 1 AA2 3 TYR A 224 GLU A 228 0 SHEET 2 AA2 3 TYR A 234 GLY A 238 -1 O VAL A 237 N ASP A 225 SHEET 3 AA2 3 VAL A 298 VAL A 301 -1 O THR A 299 N ALA A 236 SHEET 1 AA3 2 PHE A 319 GLU A 321 0 SHEET 2 AA3 2 TRP A 326 PRO A 328 -1 O GLN A 327 N TYR A 320 SHEET 1 AA4 7 ARG A 333 PHE A 334 0 SHEET 2 AA4 7 GLN B 182 ALA B 187 -1 O ASP B 185 N ARG A 333 SHEET 3 AA4 7 ILE B 107 THR B 112 1 N ARG B 110 O VAL B 184 SHEET 4 AA4 7 VAL B 79 GLU B 82 1 N LEU B 80 O ILE B 107 SHEET 5 AA4 7 ARG B 9 LEU B 13 1 N VAL B 11 O VAL B 79 SHEET 6 AA4 7 ASP B 32 ASP B 37 1 O VAL B 34 N VAL B 10 SHEET 7 AA4 7 ARG B 55 THR B 58 1 O VAL B 57 N ARG B 35 SHEET 1 AA5 3 TYR B 224 GLU B 228 0 SHEET 2 AA5 3 TYR B 234 GLY B 238 -1 O VAL B 237 N ASP B 225 SHEET 3 AA5 3 VAL B 298 PRO B 300 -1 O THR B 299 N ALA B 236 SHEET 1 AA6 2 PHE B 319 ALA B 322 0 SHEET 2 AA6 2 GLY B 325 PRO B 328 -1 O GLY B 325 N ALA B 322 CISPEP 1 ALA A 331 PRO A 332 0 -1.05 CISPEP 2 ALA B 331 PRO B 332 0 -6.26 CRYST1 181.106 79.153 59.103 90.00 91.66 90.00 C 1 2 1 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 0.005522 0.000000 0.000160 0.00000 SCALE2 0.000000 0.012634 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016927 0.00000