HEADER LYASE 19-AUG-14 4R43 TITLE CRYSTAL STRUCTURE ANALYSIS OF MTB PEPCK COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOENOLPYRUVATE CARBOXYKINASE [GTP]; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEP CARBOXYKINASE, PEPCK; COMPND 5 EC: 4.1.1.32; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RV; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: ATCC 25618 / H37RV; SOURCE 5 GENE: BCGT_4014, P425_00220, PCKG, RVBD_0211; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, GDP BINDING, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.BRYNDA,J.DOSTAL,I.PICHOVA,J.SNASEL,J.FANFRLIK,I.MACHOVA REVDAT 2 20-SEP-23 4R43 1 REMARK SEQADV LINK REVDAT 1 08-APR-15 4R43 0 JRNL AUTH I.MACHOVA,J.SNASEL,J.DOSTAL,J.BRYNDA,J.FANFRLIK,M.SINGH, JRNL AUTH 2 J.TARABEK,O.VANEK,L.BEDNAROVA,I.PICHOVA JRNL TITL STRUCTURAL AND FUNCTIONAL STUDIES OF PHOSPHOENOLPYRUVATE JRNL TITL 2 CARBOXYKINASE FROM MYCOBACTERIUM TUBERCULOSIS. JRNL REF PLOS ONE V. 10 20682 2015 JRNL REFN ESSN 1932-6203 JRNL PMID 25798914 JRNL DOI 10.1371/JOURNAL.PONE.0120682 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 68999 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3632 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4786 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.4920 REMARK 3 BIN FREE R VALUE SET COUNT : 253 REMARK 3 BIN FREE R VALUE : 0.5320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4644 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.67000 REMARK 3 B22 (A**2) : 0.26000 REMARK 3 B33 (A**2) : 0.40000 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): 0.118 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.100 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4848 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3249 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6604 ; 1.946 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7868 ; 1.168 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 608 ; 7.036 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 224 ;34.977 ;23.929 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 714 ;16.637 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;17.165 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 690 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5492 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1035 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 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 : BABINET MODEL WITH 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4R43 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086873. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979402 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72592 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 47.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.2400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.05 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.0.02 REMARK 200 STARTING MODEL: 3DTB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 4.6,30% PEG REMARK 280 300 , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 60.73300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.73300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 51.67900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.34800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.67900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.34800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 60.73300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 51.67900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 62.34800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 60.73300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 51.67900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 62.34800 REMARK 290 SMTRY3 8 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: 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 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 SER A 3 REMARK 465 ALA A 4 REMARK 465 THR A 5 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 ILE A 6 CG1 CG2 CD1 REMARK 470 THR A 11 OG1 CG2 REMARK 470 GLU A 25 CG CD OE1 OE2 REMARK 470 LYS A 92 CG CD CE NZ REMARK 470 LYS A 113 CD CE NZ REMARK 470 GLU A 138 CG CD OE1 OE2 REMARK 470 LYS A 164 CE NZ REMARK 470 LYS A 304 CG CD CE NZ REMARK 470 LYS A 327 CG CD CE NZ REMARK 470 THR A 379 CG2 REMARK 470 LYS A 422 CG CD CE NZ REMARK 470 THR A 423 CG2 REMARK 470 THR A 443 CG2 REMARK 470 GLU A 453 CG CD OE1 OE2 REMARK 470 LYS A 455 CG CD CE NZ REMARK 470 LYS A 486 CG CD CE NZ REMARK 470 SER A 491 OG REMARK 470 LYS A 492 CG CD CE NZ REMARK 470 THR A 537 CG2 REMARK 470 THR A 542 CG2 REMARK 470 LYS A 595 CD CE NZ 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 HIS A 66 CG HIS A 66 CD2 0.059 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 PRO A 7 C - N - CA ANGL. DEV. = 14.0 DEGREES REMARK 500 PRO A 7 C - N - CD ANGL. DEV. = -13.2 DEGREES REMARK 500 ASP A 10 CB - CG - OD2 ANGL. DEV. = 7.5 DEGREES REMARK 500 ASN A 260 C - N - CA ANGL. DEV. = -16.3 DEGREES REMARK 500 ARG A 389 NE - CZ - NH1 ANGL. DEV. = 3.0 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 THR A 11 34.92 -94.91 REMARK 500 PRO A 13 43.46 -80.86 REMARK 500 ASN A 62 109.40 -36.28 REMARK 500 CYS A 89 67.29 -109.19 REMARK 500 ASP A 139 76.94 57.70 REMARK 500 ASP A 173 21.49 -148.46 REMARK 500 ASN A 260 47.10 -102.55 REMARK 500 ASP A 296 -60.83 -151.19 REMARK 500 PHE A 318 79.52 -114.63 REMARK 500 ASN A 329 74.32 -155.25 REMARK 500 GLU A 378 -62.18 -135.52 REMARK 500 THR A 424 -55.61 79.04 REMARK 500 LYS A 455 133.58 -24.20 REMARK 500 VAL A 456 104.59 142.52 REMARK 500 MET A 464 26.71 49.17 REMARK 500 PHE A 515 -131.46 57.34 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 MN A 702 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 276 OG1 REMARK 620 2 GDP A 701 O1B 91.0 REMARK 620 3 HOH A 819 O 87.1 79.9 REMARK 620 4 HOH A 820 O 93.5 105.2 174.9 REMARK 620 5 HOH A 821 O 174.9 90.4 88.3 90.9 REMARK 620 6 HOH A 822 O 88.7 163.5 83.6 91.4 88.6 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 GDP A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 707 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RCG RELATED DB: PDB DBREF 4R43 A 1 606 UNP I6Y334 I6Y334_MYCTU 1 606 SEQADV 4R43 MET A -19 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 GLY A -18 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 SER A -17 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 SER A -16 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 HIS A -15 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 HIS A -14 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 HIS A -13 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 HIS A -12 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 HIS A -11 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 HIS A -10 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 SER A -9 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 SER A -8 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 GLY A -7 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 LEU A -6 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 VAL A -5 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 PRO A -4 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 ARG A -3 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 GLY A -2 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 SER A -1 UNP I6Y334 EXPRESSION TAG SEQADV 4R43 HIS A 0 UNP I6Y334 EXPRESSION TAG SEQRES 1 A 626 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 626 LEU VAL PRO ARG GLY SER HIS MET THR SER ALA THR ILE SEQRES 3 A 626 PRO GLY LEU ASP THR ALA PRO THR ASN HIS GLN GLY LEU SEQRES 4 A 626 LEU SER TRP VAL GLU GLU VAL ALA GLU LEU THR GLN PRO SEQRES 5 A 626 ASP ARG VAL VAL PHE THR ASP GLY SER GLU GLU GLU PHE SEQRES 6 A 626 GLN ARG LEU CYS ASP GLN LEU VAL GLU ALA GLY THR PHE SEQRES 7 A 626 ILE ARG LEU ASN PRO GLU LYS HIS LYS ASN SER TYR LEU SEQRES 8 A 626 ALA LEU SER ASP PRO SER ASP VAL ALA ARG VAL GLU SER SEQRES 9 A 626 ARG THR TYR ILE CYS SER ALA LYS GLU ILE ASP ALA GLY SEQRES 10 A 626 PRO THR ASN ASN TRP MET ASP PRO GLY GLU MET ARG SER SEQRES 11 A 626 ILE MET LYS ASP LEU TYR ARG GLY CYS MET ARG GLY ARG SEQRES 12 A 626 THR MET TYR VAL VAL PRO PHE CYS MET GLY PRO LEU GLY SEQRES 13 A 626 ALA GLU ASP PRO LYS LEU GLY VAL GLU ILE THR ASP SER SEQRES 14 A 626 GLU TYR VAL VAL VAL SER MET ARG THR MET THR ARG MET SEQRES 15 A 626 GLY LYS ALA ALA LEU GLU LYS MET GLY ASP ASP GLY PHE SEQRES 16 A 626 PHE VAL LYS ALA LEU HIS SER VAL GLY ALA PRO LEU GLU SEQRES 17 A 626 PRO GLY GLN LYS ASP VAL ALA TRP PRO CYS SER GLU THR SEQRES 18 A 626 LYS TYR ILE THR HIS PHE PRO GLU THR ARG GLU ILE TRP SEQRES 19 A 626 SER TYR GLY SER GLY TYR GLY GLY ASN ALA LEU LEU GLY SEQRES 20 A 626 LYS LYS CYS TYR SER LEU ARG ILE ALA SER ALA MET ALA SEQRES 21 A 626 HIS ASP GLU GLY TRP LEU ALA GLU HIS MET LEU ILE LEU SEQRES 22 A 626 LYS LEU ILE SER PRO GLU ASN LYS ALA TYR TYR PHE ALA SEQRES 23 A 626 ALA ALA PHE PRO SER ALA CYS GLY LYS THR ASN LEU ALA SEQRES 24 A 626 MET LEU GLN PRO THR ILE PRO GLY TRP ARG ALA GLU THR SEQRES 25 A 626 LEU GLY ASP ASP ILE ALA TRP MET ARG PHE GLY LYS ASP SEQRES 26 A 626 GLY ARG LEU TYR ALA VAL ASN PRO GLU PHE GLY PHE PHE SEQRES 27 A 626 GLY VAL ALA PRO GLY THR ASN TRP LYS SER ASN PRO ASN SEQRES 28 A 626 ALA MET ARG THR ILE ALA ALA GLY ASN THR VAL PHE THR SEQRES 29 A 626 ASN VAL ALA LEU THR ASP ASP GLY ASP VAL TRP TRP GLU SEQRES 30 A 626 GLY LEU GLU GLY ASP PRO GLN HIS LEU ILE ASP TRP LYS SEQRES 31 A 626 GLY ASN ASP TRP TYR PHE ARG GLU THR GLU THR ASN ALA SEQRES 32 A 626 ALA HIS PRO ASN SER ARG TYR CYS THR PRO MET SER GLN SEQRES 33 A 626 CYS PRO ILE LEU ALA PRO GLU TRP ASP ASP PRO GLN GLY SEQRES 34 A 626 VAL PRO ILE SER GLY ILE LEU PHE GLY GLY ARG ARG LYS SEQRES 35 A 626 THR THR VAL PRO LEU VAL THR GLU ALA ARG ASP TRP GLN SEQRES 36 A 626 HIS GLY VAL PHE ILE GLY ALA THR LEU GLY SER GLU GLN SEQRES 37 A 626 THR ALA ALA ALA GLU GLY LYS VAL GLY ASN VAL ARG ARG SEQRES 38 A 626 ASP PRO MET ALA MET LEU PRO PHE LEU GLY TYR ASN VAL SEQRES 39 A 626 GLY ASP TYR PHE GLN HIS TRP ILE ASN LEU GLY LYS HIS SEQRES 40 A 626 ALA ASP GLU SER LYS LEU PRO LYS VAL PHE PHE VAL ASN SEQRES 41 A 626 TRP PHE ARG ARG GLY ASP ASP GLY ARG PHE LEU TRP PRO SEQRES 42 A 626 GLY PHE GLY GLU ASN SER ARG VAL LEU LYS TRP ILE VAL SEQRES 43 A 626 ASP ARG ILE GLU HIS LYS ALA GLY GLY ALA THR THR PRO SEQRES 44 A 626 ILE GLY THR VAL PRO ALA VAL GLU ASP LEU ASP LEU ASP SEQRES 45 A 626 GLY LEU ASP VAL ASP ALA ALA ASP VAL ALA ALA ALA LEU SEQRES 46 A 626 ALA VAL ASP ALA ASP GLU TRP ARG GLN GLU LEU PRO LEU SEQRES 47 A 626 ILE GLU GLU TRP LEU GLN PHE VAL GLY GLU LYS LEU PRO SEQRES 48 A 626 THR GLY VAL LYS ASP GLU PHE ASP ALA LEU LYS GLU ARG SEQRES 49 A 626 LEU GLY HET GDP A 701 28 HET MN A 702 1 HET PEG A 703 7 HET PEG A 704 7 HET PEG A 705 7 HET PEG A 706 7 HET PO4 A 707 5 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PO4 PHOSPHATE ION FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MN MN 2+ FORMUL 4 PEG 4(C4 H10 O3) FORMUL 8 PO4 O4 P 3- FORMUL 9 HOH *96(H2 O) HELIX 1 1 HIS A 16 GLN A 31 1 16 HELIX 2 2 SER A 41 ALA A 55 1 15 HELIX 3 3 VAL A 82 SER A 84 5 3 HELIX 4 4 LYS A 92 ALA A 96 5 5 HELIX 5 5 ASP A 104 ARG A 117 1 14 HELIX 6 6 SER A 149 THR A 160 1 12 HELIX 7 7 GLY A 163 GLY A 171 1 9 HELIX 8 8 TYR A 220 ALA A 224 5 5 HELIX 9 9 LEU A 233 GLY A 244 1 12 HELIX 10 10 GLY A 274 MET A 280 1 7 HELIX 11 11 ASN A 329 ALA A 338 1 10 HELIX 12 12 SER A 395 CYS A 397 5 3 HELIX 13 13 ALA A 401 ASP A 406 5 6 HELIX 14 14 ASP A 433 THR A 443 1 11 HELIX 15 15 PRO A 463 MET A 466 5 4 HELIX 16 16 ASN A 473 HIS A 487 1 15 HELIX 17 17 ASP A 489 LEU A 493 5 5 HELIX 18 18 GLY A 514 GLU A 517 5 4 HELIX 19 19 ASN A 518 GLU A 530 1 13 HELIX 20 20 ALA A 545 LEU A 549 5 5 HELIX 21 21 ASP A 557 ALA A 566 1 10 HELIX 22 22 ASP A 568 GLY A 587 1 20 HELIX 23 23 GLU A 588 LEU A 590 5 3 HELIX 24 24 PRO A 591 GLY A 606 1 16 SHEET 1 A 7 ARG A 34 PHE A 37 0 SHEET 2 A 7 THR A 124 MET A 132 1 O MET A 125 N ARG A 34 SHEET 3 A 7 LYS A 141 THR A 147 -1 O LYS A 141 N MET A 132 SHEET 4 A 7 VAL A 177 SER A 182 1 O ALA A 179 N ILE A 146 SHEET 5 A 7 GLU A 212 TYR A 216 1 O SER A 215 N LEU A 180 SHEET 6 A 7 TYR A 203 PHE A 207 -1 N PHE A 207 O GLU A 212 SHEET 7 A 7 THR A 86 ILE A 88 1 N TYR A 87 O ILE A 204 SHEET 1 B 3 ARG A 34 PHE A 37 0 SHEET 2 B 3 THR A 124 MET A 132 1 O MET A 125 N ARG A 34 SHEET 3 B 3 ARG A 161 MET A 162 -1 O ARG A 161 N CYS A 131 SHEET 1 C 5 PHE A 58 ARG A 60 0 SHEET 2 C 5 TYR A 70 ALA A 72 -1 O LEU A 71 N ILE A 59 SHEET 3 C 5 VAL A 342 THR A 344 1 O PHE A 343 N ALA A 72 SHEET 4 C 5 ARG A 389 PRO A 393 -1 O ARG A 389 N THR A 344 SHEET 5 C 5 GLY A 316 VAL A 320 -1 N PHE A 317 O THR A 392 SHEET 1 D 7 LEU A 246 GLU A 248 0 SHEET 2 D 7 ALA A 298 PHE A 302 -1 O ALA A 298 N GLU A 248 SHEET 3 D 7 LEU A 308 VAL A 311 -1 O VAL A 311 N TRP A 299 SHEET 4 D 7 VAL A 410 GLY A 418 -1 O ILE A 412 N LEU A 308 SHEET 5 D 7 ALA A 262 ALA A 268 1 N TYR A 264 O SER A 413 SHEET 6 D 7 LEU A 251 ILE A 256 -1 N LEU A 255 O TYR A 263 SHEET 7 D 7 ARG A 289 ASP A 295 -1 O ARG A 289 N ILE A 256 SHEET 1 E 6 LEU A 246 GLU A 248 0 SHEET 2 E 6 ALA A 298 PHE A 302 -1 O ALA A 298 N GLU A 248 SHEET 3 E 6 LEU A 308 VAL A 311 -1 O VAL A 311 N TRP A 299 SHEET 4 E 6 VAL A 410 GLY A 418 -1 O ILE A 412 N LEU A 308 SHEET 5 E 6 LYS A 495 VAL A 499 1 O PHE A 497 N ILE A 415 SHEET 6 E 6 VAL A 428 GLU A 430 -1 N THR A 429 O PHE A 498 SHEET 1 F 2 ALA A 347 LEU A 348 0 SHEET 2 F 2 VAL A 354 TRP A 355 -1 O TRP A 355 N ALA A 347 SHEET 1 G 2 HIS A 365 ILE A 367 0 SHEET 2 G 2 ASP A 373 TYR A 375 -1 O TRP A 374 N LEU A 366 SHEET 1 H 2 GLY A 445 SER A 446 0 SHEET 2 H 2 ARG A 460 ARG A 461 -1 O ARG A 460 N SER A 446 SHEET 1 I 2 ALA A 536 THR A 538 0 SHEET 2 I 2 GLY A 541 VAL A 543 -1 O VAL A 543 N ALA A 536 LINK OG1 THR A 276 MN MN A 702 1555 1555 2.03 LINK O1B GDP A 701 MN MN A 702 1555 1555 2.20 LINK MN MN A 702 O HOH A 819 1555 1555 2.04 LINK MN MN A 702 O HOH A 820 1555 1555 2.23 LINK MN MN A 702 O HOH A 821 1555 1555 2.27 LINK MN MN A 702 O HOH A 822 1555 1555 2.25 CISPEP 1 PRO A 7 GLY A 8 0 -21.79 CISPEP 2 LYS A 455 VAL A 456 0 -13.58 SITE 1 AC1 22 PRO A 270 ALA A 272 CYS A 273 GLY A 274 SITE 2 AC1 22 LYS A 275 THR A 276 ASN A 277 ASP A 362 SITE 3 AC1 22 PHE A 376 ARG A 377 ARG A 420 TRP A 501 SITE 4 AC1 22 PHE A 502 PHE A 510 GLY A 514 PHE A 515 SITE 5 AC1 22 ASN A 518 MN A 702 HOH A 812 HOH A 819 SITE 6 AC1 22 HOH A 821 HOH A 841 SITE 1 AC2 6 THR A 276 GDP A 701 HOH A 819 HOH A 820 SITE 2 AC2 6 HOH A 821 HOH A 822 SITE 1 AC3 3 ARG A 301 TYR A 309 PRO A 407 SITE 1 AC4 3 ARG A 307 ILE A 412 SER A 413 SITE 1 AC5 3 ARG A 157 ASN A 340 HOH A 829 SITE 1 AC6 5 PRO A 283 THR A 284 ILE A 285 GLY A 287 SITE 2 AC6 5 TRP A 288 SITE 1 AC7 7 LYS A 229 HIS A 249 SER A 271 LYS A 275 SITE 2 AC7 7 ASP A 296 HOH A 820 HOH A 821 CRYST1 103.358 124.696 121.466 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009675 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008020 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008233 0.00000