HEADER LYASE 16-SEP-14 4RCG TITLE CRYSTAL STRUCTURE ANALYSIS OF MTB PEPCK WITHOUT MN+2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOENOLPYRUVATE CARBOXYKINASE [GTP]; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 8-606; COMPND 5 SYNONYM: PEP CARBOXYKINASE, PEPCK; COMPND 6 EC: 4.1.1.32; COMPND 7 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: PCKG, P425_00220, RVBD_0211; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHOENOLPYRUVATE CARBOXYKINASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.BRYNDA,J.DOSTAL,J.SNASEL,J.FANFRLIK,I.PICHOVA,I.MACHOVA REVDAT 2 20-SEP-23 4RCG 1 REMARK SEQADV REVDAT 1 08-APR-15 4RCG 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. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 23134 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1218 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) : 2.61 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1441 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.3980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4530 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.31000 REMARK 3 B22 (A**2) : -3.47000 REMARK 3 B33 (A**2) : -1.84000 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): 0.543 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.322 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.238 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.238 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4704 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3127 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6401 ; 1.890 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7567 ; 1.031 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 590 ; 8.417 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 214 ;35.992 ;24.019 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 675 ;18.652 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;21.621 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 668 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5344 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1004 ; 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 4RCG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000087173. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24338 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.13500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.070 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: 4R43 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, 30%PEG 300, PH REMARK 280 4.6, 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 60.81750 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 60.81750 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 52.20600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.13850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 52.20600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.13850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 60.81750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 52.20600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 62.13850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 60.81750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 52.20600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 62.13850 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 465 ILE A 6 REMARK 465 PRO A 7 REMARK 465 ALA A 451 REMARK 465 ALA A 452 REMARK 465 GLU A 453 REMARK 465 GLY A 454 REMARK 465 LYS A 455 REMARK 465 VAL A 456 REMARK 465 SER A 457 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 LEU A 9 CG CD1 CD2 REMARK 470 THR A 11 OG1 CG2 REMARK 470 GLU A 24 CG CD OE1 OE2 REMARK 470 GLU A 25 CG CD OE1 OE2 REMARK 470 GLU A 43 CG CD OE1 OE2 REMARK 470 LYS A 67 CG CD CE NZ REMARK 470 LEU A 73 CD2 REMARK 470 ARG A 81 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 83 CG CD OE1 OE2 REMARK 470 ARG A 85 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 87 OH REMARK 470 LYS A 92 CG CD CE NZ REMARK 470 ILE A 111 CG2 REMARK 470 LYS A 113 CD CE NZ REMARK 470 GLU A 138 CG CD OE1 OE2 REMARK 470 ILE A 146 CG2 REMARK 470 VAL A 154 CG2 REMARK 470 LYS A 164 CG CD CE NZ REMARK 470 HIS A 206 CD2 NE2 REMARK 470 ARG A 211 NH1 NH2 REMARK 470 HIS A 241 CD2 NE2 REMARK 470 LYS A 304 CG CD CE NZ REMARK 470 ASP A 305 CG OD1 OD2 REMARK 470 LYS A 327 CG CD CE NZ REMARK 470 ASN A 331 ND2 REMARK 470 ILE A 336 CG2 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 GLN A 448 CG CD OE1 NE2 REMARK 470 LEU A 470 CD2 REMARK 470 LYS A 486 CG CD CE NZ REMARK 470 LYS A 492 CG CD CE NZ REMARK 470 LYS A 532 CE NZ REMARK 470 THR A 537 CG2 REMARK 470 THR A 542 CG2 REMARK 470 ARG A 573 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 576 CD1 CD2 REMARK 470 ILE A 579 CG2 REMARK 470 LYS A 595 CG CD CE NZ REMARK 470 LEU A 605 CD2 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 OD1 ASP A 406 OE1 GLN A 408 2.05 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 TRP A 356 CE2 TRP A 356 CD2 0.079 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 GLU A 150 OE1 - CD - OE2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG A 528 CG - CD - NE ANGL. DEV. = -16.5 DEGREES REMARK 500 ARG A 528 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 THR A 11 57.04 -112.82 REMARK 500 GLN A 31 53.08 70.62 REMARK 500 PRO A 76 -16.52 -46.61 REMARK 500 ALA A 80 -165.47 -172.13 REMARK 500 ARG A 81 -134.56 62.05 REMARK 500 VAL A 82 61.07 60.82 REMARK 500 CYS A 89 67.55 -105.85 REMARK 500 ARG A 117 109.98 -54.44 REMARK 500 LEU A 135 -34.20 119.29 REMARK 500 ARG A 161 99.64 -68.72 REMARK 500 ASP A 173 11.62 -151.09 REMARK 500 LYS A 229 -34.42 -140.87 REMARK 500 ASP A 296 -49.40 -141.95 REMARK 500 ASN A 329 78.54 -157.91 REMARK 500 ARG A 377 19.50 50.94 REMARK 500 GLU A 378 -66.01 -130.50 REMARK 500 THR A 424 -36.54 91.64 REMARK 500 ASP A 433 -178.37 -170.85 REMARK 500 GLN A 448 -165.17 164.92 REMARK 500 THR A 449 175.97 63.51 REMARK 500 MET A 464 34.68 39.74 REMARK 500 HIS A 487 45.69 -92.85 REMARK 500 PHE A 515 -132.29 54.26 REMARK 500 GLU A 530 39.73 -90.81 REMARK 500 HIS A 531 42.93 33.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 80 ARG A 81 119.67 REMARK 500 GLY A 190 GLN A 191 -145.41 REMARK 500 ASP A 305 GLY A 306 -49.57 REMARK 500 REMARK 500 REMARK: NULL 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 MG 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4R43 RELATED DB: PDB DBREF 4RCG A 1 606 UNP I6Y334 I6Y334_MYCTU 1 606 SEQADV 4RCG MET A -19 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG GLY A -18 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG SER A -17 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG SER A -16 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG HIS A -15 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG HIS A -14 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG HIS A -13 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG HIS A -12 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG HIS A -11 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG HIS A -10 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG SER A -9 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG SER A -8 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG GLY A -7 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG LEU A -6 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG VAL A -5 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG PRO A -4 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG ARG A -3 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG GLY A -2 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG SER A -1 UNP I6Y334 EXPRESSION TAG SEQADV 4RCG 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 SER 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 ALA 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 MG A 702 1 HET PEG A 703 7 HET PEG A 704 7 HET PEG A 705 7 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ FORMUL 4 PEG 3(C4 H10 O3) FORMUL 7 HOH *21(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 MET A 170 1 8 HELIX 8 8 TYR A 220 LEU A 225 1 6 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 GLY A 514 GLU A 517 5 4 HELIX 18 18 ASN A 518 GLU A 530 1 13 HELIX 19 19 ALA A 545 LEU A 549 5 5 HELIX 20 20 ASP A 557 LEU A 565 1 9 HELIX 21 21 ASP A 568 GLY A 587 1 20 HELIX 22 22 GLU A 588 LEU A 590 5 3 HELIX 23 23 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 VAL A 127 N VAL A 36 SHEET 3 A 7 LYS A 141 THR A 147 -1 O GLY A 143 N PHE A 130 SHEET 4 A 7 VAL A 177 SER A 182 1 O VAL A 177 N LEU A 142 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 VAL A 127 N VAL A 36 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 TYR A 70 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 TYR A 309 N ARG A 301 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 ALA A 266 O LEU A 416 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 GLY A 294 -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 TYR A 309 N ARG A 301 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 LYS A 495 N SER A 413 SHEET 6 E 6 VAL A 428 GLU A 430 -1 N THR A 429 O PHE A 498 SHEET 1 F 4 VAL A 354 TRP A 355 0 SHEET 2 F 4 ALA A 347 THR A 349 -1 N ALA A 347 O TRP A 355 SHEET 3 F 4 HIS A 365 ILE A 367 -1 O ILE A 367 N LEU A 348 SHEET 4 F 4 ASP A 373 TYR A 375 -1 O TRP A 374 N LEU A 366 SHEET 1 G 2 GLY A 445 SER A 446 0 SHEET 2 G 2 ARG A 460 ARG A 461 -1 O ARG A 460 N SER A 446 SHEET 1 H 2 ALA A 536 THR A 538 0 SHEET 2 H 2 GLY A 541 VAL A 543 -1 O VAL A 543 N ALA A 536 CISPEP 1 GLU A 259 ASN A 260 0 -25.19 CISPEP 2 GLU A 447 GLN A 448 0 1.67 SITE 1 AC1 18 PRO A 270 SER A 271 ALA A 272 CYS A 273 SITE 2 AC1 18 GLY A 274 LYS A 275 THR A 276 ASN A 277 SITE 3 AC1 18 ASP A 362 ARG A 377 ARG A 420 TRP A 501 SITE 4 AC1 18 PHE A 502 GLY A 514 PHE A 515 ASN A 518 SITE 5 AC1 18 HOH A 814 HOH A 817 SITE 1 AC2 2 CYS A 273 SER A 446 SITE 1 AC3 2 ARG A 301 PRO A 407 SITE 1 AC4 4 ARG A 307 SER A 413 ALA A 491 LYS A 492 SITE 1 AC5 4 GLU A 42 ASN A 68 ARG A 157 ASN A 340 CRYST1 104.412 124.277 121.635 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 0.009577 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008047 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008221 0.00000