HEADER TRANSFERASE 06-FEB-15 4Y12
TITLE CRYSTAL STRUCTURE OF THE S/T PROTEIN KINASE PKNG FROM MYCOBACTERIUM
TITLE 2 TUBERCULOSIS IN COMPLEX WITH AGS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PKNG;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 74-405;
COMPND 5 EC: 2.7.11.1;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 /
SOURCE 3 H37RV);
SOURCE 4 ORGANISM_TAXID: 83332;
SOURCE 5 GENE: PKNG, RV0410C, MTCY22G10.06C;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008
KEYWDS S/T PROTEIN KINASE, PKNG, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.N.LISA,P.M.ALZARI
REVDAT 3 10-JAN-24 4Y12 1 LINK
REVDAT 2 10-JUN-15 4Y12 1 JRNL
REVDAT 1 20-MAY-15 4Y12 0
JRNL AUTH M.N.LISA,M.GIL,G.ANDRE-LEROUX,N.BARILONE,R.DURAN,R.M.BIONDI,
JRNL AUTH 2 P.M.ALZARI
JRNL TITL MOLECULAR BASIS OF THE ACTIVITY AND THE REGULATION OF THE
JRNL TITL 2 EUKARYOTIC-LIKE S/T PROTEIN KINASE PKNG FROM MYCOBACTERIUM
JRNL TITL 3 TUBERCULOSIS.
JRNL REF STRUCTURE V. 23 1039 2015
JRNL REFN ISSN 0969-2126
JRNL PMID 25960409
JRNL DOI 10.1016/J.STR.2015.04.001
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.11.4
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.90
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6
REMARK 3 NUMBER OF REFLECTIONS : 23246
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) : 0.197
REMARK 3 R VALUE (WORKING SET) : 0.196
REMARK 3 FREE R VALUE : 0.212
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.210
REMARK 3 FREE R VALUE TEST SET COUNT : 1210
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 12
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.98
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.62
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2771
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2387
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2625
REMARK 3 BIN R VALUE (WORKING SET) : 0.2369
REMARK 3 BIN FREE R VALUE : 0.2725
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.27
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 146
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2379
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 34
REMARK 3 SOLVENT ATOMS : 171
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 33.42
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.82
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 6.44010
REMARK 3 B22 (A**2) : -11.73470
REMARK 3 B33 (A**2) : 5.29460
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -1.84670
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.300
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.171
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.136
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.167
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.135
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 2468 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 3383 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 793 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 47 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 383 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 2468 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 328 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 2937 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.05
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.96
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.98
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 4
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: { A|83 - A|97 }
REMARK 3 ORIGIN FOR THE GROUP (A): -16.6769 20.3009 -32.8816
REMARK 3 T TENSOR
REMARK 3 T11: -0.0368 T22: 0.1240
REMARK 3 T33: -0.0350 T12: -0.0364
REMARK 3 T13: 0.1019 T23: -0.0911
REMARK 3 L TENSOR
REMARK 3 L11: 0.3593 L22: 2.6029
REMARK 3 L33: 0.0356 L12: -0.0881
REMARK 3 L13: 0.1528 L23: 1.0587
REMARK 3 S TENSOR
REMARK 3 S11: -0.0024 S12: -0.0314 S13: 0.0441
REMARK 3 S21: 0.0004 S22: 0.0400 S23: -0.1000
REMARK 3 S31: -0.1685 S32: -0.0111 S33: -0.0376
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: { A|98 - A|137 }
REMARK 3 ORIGIN FOR THE GROUP (A): 10.9636 13.9609 -44.8795
REMARK 3 T TENSOR
REMARK 3 T11: -0.1626 T22: 0.1111
REMARK 3 T33: -0.1310 T12: -0.1079
REMARK 3 T13: -0.0157 T23: 0.0336
REMARK 3 L TENSOR
REMARK 3 L11: 6.4831 L22: 6.8499
REMARK 3 L33: 6.5974 L12: 0.5131
REMARK 3 L13: 1.5681 L23: 2.9843
REMARK 3 S TENSOR
REMARK 3 S11: 0.0034 S12: 0.0432 S13: 0.2637
REMARK 3 S21: -0.1582 S22: -0.0544 S23: -0.0828
REMARK 3 S31: 0.0328 S32: 0.1920 S33: 0.0509
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: { A|138 - A|236 }
REMARK 3 ORIGIN FOR THE GROUP (A): -6.9495 1.4986 -36.7610
REMARK 3 T TENSOR
REMARK 3 T11: -0.1132 T22: 0.1448
REMARK 3 T33: -0.1310 T12: -0.1428
REMARK 3 T13: 0.0259 T23: -0.0763
REMARK 3 L TENSOR
REMARK 3 L11: 2.1265 L22: 2.3287
REMARK 3 L33: 2.4654 L12: -0.8083
REMARK 3 L13: 1.6733 L23: -1.8621
REMARK 3 S TENSOR
REMARK 3 S11: 0.2240 S12: 0.1665 S13: -0.0673
REMARK 3 S21: -0.0410 S22: -0.2772 S23: 0.0559
REMARK 3 S31: 0.3301 S32: -0.0114 S33: 0.0533
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: { A|237 - A|404 }
REMARK 3 ORIGIN FOR THE GROUP (A): 9.1823 2.9290 -14.2373
REMARK 3 T TENSOR
REMARK 3 T11: -0.1116 T22: 0.0151
REMARK 3 T33: -0.1110 T12: -0.0187
REMARK 3 T13: 0.0194 T23: -0.0031
REMARK 3 L TENSOR
REMARK 3 L11: 2.0783 L22: 1.3724
REMARK 3 L33: 4.4203 L12: -0.2566
REMARK 3 L13: -0.9338 L23: -0.2733
REMARK 3 S TENSOR
REMARK 3 S11: -0.0992 S12: -0.3028 S13: -0.0540
REMARK 3 S21: 0.0110 S22: 0.0405 S23: -0.1519
REMARK 3 S31: 0.0987 S32: 0.3040 S33: 0.0587
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4Y12 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-FEB-15.
REMARK 100 THE DEPOSITION ID IS D_1000206671.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 20-FEB-12
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SOLEIL
REMARK 200 BEAMLINE : PROXIMA 1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.28189
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 : XDS 2.11.4
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23248
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 37.370
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 200 DATA REDUNDANCY : 7.400
REMARK 200 R MERGE (I) : 0.07300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4
REMARK 200 DATA REDUNDANCY IN SHELL : 7.20
REMARK 200 R MERGE FOR SHELL (I) : 0.77400
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600
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: 4Y0X
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 32.87
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, 35% W/V PEG 4000, 200 MM
REMARK 280 CACL2, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
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 37.72600
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.59150
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.72600
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.59150
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1090 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 15580 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 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 31
REMARK 465 GLY A 32
REMARK 465 SER A 33
REMARK 465 SER A 34
REMARK 465 HIS A 35
REMARK 465 HIS A 36
REMARK 465 HIS A 37
REMARK 465 HIS A 38
REMARK 465 HIS A 39
REMARK 465 HIS A 40
REMARK 465 SER A 41
REMARK 465 SER A 42
REMARK 465 GLY A 43
REMARK 465 LEU A 44
REMARK 465 VAL A 45
REMARK 465 PRO A 46
REMARK 465 ARG A 47
REMARK 465 GLY A 48
REMARK 465 SER A 49
REMARK 465 HIS A 50
REMARK 465 MET A 51
REMARK 465 ALA A 52
REMARK 465 SER A 53
REMARK 465 MET A 54
REMARK 465 THR A 55
REMARK 465 GLY A 56
REMARK 465 GLY A 57
REMARK 465 GLN A 58
REMARK 465 GLN A 59
REMARK 465 MET A 60
REMARK 465 GLY A 61
REMARK 465 ARG A 62
REMARK 465 GLY A 63
REMARK 465 SER A 64
REMARK 465 GLU A 65
REMARK 465 PHE A 66
REMARK 465 GLU A 67
REMARK 465 ASN A 68
REMARK 465 LEU A 69
REMARK 465 TYR A 70
REMARK 465 PHE A 71
REMARK 465 GLN A 72
REMARK 465 GLY A 73
REMARK 465 LEU A 74
REMARK 465 GLY A 75
REMARK 465 GLY A 76
REMARK 465 GLY A 77
REMARK 465 LEU A 78
REMARK 465 VAL A 79
REMARK 465 GLU A 80
REMARK 465 ILE A 81
REMARK 465 PRO A 82
REMARK 465 GLY A 405
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 VAL A 98 CG1 CG2
REMARK 470 LYS A 103 CG CD CE NZ
REMARK 470 ASP A 117 CG OD1 OD2
REMARK 470 SER A 118 OG
REMARK 470 GLU A 119 CG CD OE1 OE2
REMARK 470 THR A 120 OG1 CG2
REMARK 470 LYS A 121 CG CD CE NZ
REMARK 470 TYR A 130 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 VAL A 173 CG1 CG2
REMARK 470 ASN A 174 CG OD1 ND2
REMARK 470 VAL A 184 CG1 CG2
REMARK 470 SER A 186 OG
REMARK 470 GLU A 190 CG CD OE1 OE2
REMARK 470 MET A 194 CG SD CE
REMARK 470 GLU A 198 CG CD OE1 OE2
REMARK 470 GLU A 204 CG CD OE1 OE2
REMARK 470 GLU A 218 CG CD OE1 OE2
REMARK 470 ASP A 221 CG OD1 OD2
REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2
REMARK 470 ASP A 225 CG OD1 OD2
REMARK 470 LYS A 244 CG CD CE NZ
REMARK 470 GLU A 286 CG CD OE1 OE2
REMARK 470 ARG A 299 CG CD NE CZ NH1 NH2
REMARK 470 ASP A 341 CG OD1 OD2
REMARK 470 ARG A 345 CG CD NE CZ NH1 NH2
REMARK 470 ARG A 348 CG CD NE CZ NH1 NH2
REMARK 470 GLU A 355 CG CD OE1 OE2
REMARK 470 ASP A 356 CG OD1 OD2
REMARK 470 ASP A 357 CG OD1 OD2
REMARK 470 LYS A 361 CG CD CE NZ
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 LYS A 244 -34.84 -37.63
REMARK 500 ASN A 275 -9.34 68.13
REMARK 500 ILE A 292 -169.93 -118.35
REMARK 500 ASP A 293 70.98 53.23
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 765 DISTANCE = 5.82 ANGSTROMS
REMARK 525 HOH A 767 DISTANCE = 7.48 ANGSTROMS
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 ZN A 502 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 106 SG
REMARK 620 2 CYS A 109 SG 109.2
REMARK 620 3 CYS A 128 SG 109.6 104.9
REMARK 620 4 CYS A 131 SG 99.2 117.8 115.9
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 503 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A 281 OD1
REMARK 620 2 ASP A 293 OD2 87.2
REMARK 620 3 AGS A 501 O3B 161.1 74.9
REMARK 620 4 AGS A 501 O2A 95.3 100.7 82.5
REMARK 620 5 HOH A 607 O 99.0 161.1 99.9 96.5
REMARK 620 6 HOH A 628 O 96.8 75.4 84.6 167.1 86.1
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 504 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 293 OD1
REMARK 620 2 ASP A 293 OD2 48.8
REMARK 620 3 AGS A 501 O2G 65.4 71.7
REMARK 620 4 HOH A 602 O 123.3 80.2 126.4
REMARK 620 5 HOH A 612 O 66.0 69.1 130.2 74.9
REMARK 620 6 HOH A 629 O 123.2 141.6 145.1 79.8 74.2
REMARK 620 7 HOH A 693 O 79.7 123.6 66.3 156.1 113.9 81.5
REMARK 620 N 1 2 3 4 5 6
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue AGS A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 504
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4Y0X RELATED DB: PDB
REMARK 900 4Y0X CONTAINS THE SAME PROTEIN IN COMPLEX WITH ADP
DBREF 4Y12 A 74 405 UNP P9WI73 PKNG_MYCTU 74 405
SEQADV 4Y12 MET A 31 UNP P9WI73 INITIATING METHIONINE
SEQADV 4Y12 GLY A 32 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 SER A 33 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 SER A 34 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 HIS A 35 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 HIS A 36 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 HIS A 37 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 HIS A 38 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 HIS A 39 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 HIS A 40 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 SER A 41 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 SER A 42 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 GLY A 43 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 LEU A 44 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 VAL A 45 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 PRO A 46 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 ARG A 47 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 GLY A 48 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 SER A 49 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 HIS A 50 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 MET A 51 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 ALA A 52 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 SER A 53 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 MET A 54 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 THR A 55 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 GLY A 56 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 GLY A 57 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 GLN A 58 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 GLN A 59 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 MET A 60 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 GLY A 61 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 ARG A 62 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 GLY A 63 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 SER A 64 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 GLU A 65 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 PHE A 66 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 GLU A 67 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 ASN A 68 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 LEU A 69 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 TYR A 70 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 PHE A 71 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 GLN A 72 UNP P9WI73 EXPRESSION TAG
SEQADV 4Y12 GLY A 73 UNP P9WI73 EXPRESSION TAG
SEQRES 1 A 375 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY
SEQRES 2 A 375 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY
SEQRES 3 A 375 GLY GLN GLN MET GLY ARG GLY SER GLU PHE GLU ASN LEU
SEQRES 4 A 375 TYR PHE GLN GLY LEU GLY GLY GLY LEU VAL GLU ILE PRO
SEQRES 5 A 375 ARG ALA PRO ASP ILE ASP PRO LEU GLU ALA LEU MET THR
SEQRES 6 A 375 ASN PRO VAL VAL PRO GLU SER LYS ARG PHE CYS TRP ASN
SEQRES 7 A 375 CYS GLY ARG PRO VAL GLY ARG SER ASP SER GLU THR LYS
SEQRES 8 A 375 GLY ALA SER GLU GLY TRP CYS PRO TYR CYS GLY SER PRO
SEQRES 9 A 375 TYR SER PHE LEU PRO GLN LEU ASN PRO GLY ASP ILE VAL
SEQRES 10 A 375 ALA GLY GLN TYR GLU VAL LYS GLY CYS ILE ALA HIS GLY
SEQRES 11 A 375 GLY LEU GLY TRP ILE TYR LEU ALA LEU ASP ARG ASN VAL
SEQRES 12 A 375 ASN GLY ARG PRO VAL VAL LEU LYS GLY LEU VAL HIS SER
SEQRES 13 A 375 GLY ASP ALA GLU ALA GLN ALA MET ALA MET ALA GLU ARG
SEQRES 14 A 375 GLN PHE LEU ALA GLU VAL VAL HIS PRO SER ILE VAL GLN
SEQRES 15 A 375 ILE PHE ASN PHE VAL GLU HIS THR ASP ARG HIS GLY ASP
SEQRES 16 A 375 PRO VAL GLY TYR ILE VAL MET GLU TYR VAL GLY GLY GLN
SEQRES 17 A 375 SER LEU LYS ARG SER LYS GLY GLN LYS LEU PRO VAL ALA
SEQRES 18 A 375 GLU ALA ILE ALA TYR LEU LEU GLU ILE LEU PRO ALA LEU
SEQRES 19 A 375 SER TYR LEU HIS SER ILE GLY LEU VAL TYR ASN ASP LEU
SEQRES 20 A 375 LYS PRO GLU ASN ILE MET LEU THR GLU GLU GLN LEU LYS
SEQRES 21 A 375 LEU ILE ASP LEU GLY ALA VAL SER ARG ILE ASN SER PHE
SEQRES 22 A 375 GLY TYR LEU TYR GLY THR PRO GLY PHE GLN ALA PRO GLU
SEQRES 23 A 375 ILE VAL ARG THR GLY PRO THR VAL ALA THR ASP ILE TYR
SEQRES 24 A 375 THR VAL GLY ARG THR LEU ALA ALA LEU THR LEU ASP LEU
SEQRES 25 A 375 PRO THR ARG ASN GLY ARG TYR VAL ASP GLY LEU PRO GLU
SEQRES 26 A 375 ASP ASP PRO VAL LEU LYS THR TYR ASP SER TYR GLY ARG
SEQRES 27 A 375 LEU LEU ARG ARG ALA ILE ASP PRO ASP PRO ARG GLN ARG
SEQRES 28 A 375 PHE THR THR ALA GLU GLU MET SER ALA GLN LEU THR GLY
SEQRES 29 A 375 VAL LEU ARG GLU VAL VAL ALA GLN ASP THR GLY
HET AGS A 501 31
HET ZN A 502 1
HET MG A 503 1
HET MG A 504 1
HETNAM AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
HETNAM ZN ZINC ION
HETNAM MG MAGNESIUM ION
HETSYN AGS ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
HETSYN 2 AGS ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-
HETSYN 3 AGS DIPHOSPHATE MONOTHIOPHOSPHATE
FORMUL 2 AGS C10 H16 N5 O12 P3 S
FORMUL 3 ZN ZN 2+
FORMUL 4 MG 2(MG 2+)
FORMUL 6 HOH *171(H2 O)
HELIX 1 AA1 LEU A 90 MET A 94 5 5
HELIX 2 AA2 PRO A 100 ARG A 104 5 5
HELIX 3 AA3 ASP A 188 GLN A 200 1 13
HELIX 4 AA4 PHE A 201 VAL A 205 5 5
HELIX 5 AA5 PRO A 249 ILE A 270 1 22
HELIX 6 AA6 LYS A 278 GLU A 280 5 3
HELIX 7 AA7 ASP A 293 VAL A 297 5 5
HELIX 8 AA8 GLU A 316 GLY A 321 1 6
HELIX 9 AA9 THR A 323 LEU A 340 1 18
HELIX 10 AB1 ASP A 357 TYR A 363 1 7
HELIX 11 AB2 TYR A 363 ILE A 374 1 12
HELIX 12 AB3 ASP A 377 ARG A 381 5 5
HELIX 13 AB4 THR A 384 ASP A 403 1 20
SHEET 1 AA1 2 GLU A 125 TRP A 127 0
SHEET 2 AA1 2 PRO A 134 SER A 136 -1 O TYR A 135 N GLY A 126
SHEET 1 AA2 6 ILE A 146 VAL A 147 0
SHEET 2 AA2 6 TYR A 151 GLY A 160 -1 O TYR A 151 N VAL A 147
SHEET 3 AA2 6 GLY A 163 ASP A 170 -1 O ILE A 165 N ILE A 157
SHEET 4 AA2 6 PRO A 177 GLY A 182 -1 O VAL A 178 N ALA A 168
SHEET 5 AA2 6 PRO A 226 GLU A 233 -1 O MET A 232 N VAL A 179
SHEET 6 AA2 6 ILE A 213 THR A 220 -1 N HIS A 219 O VAL A 227
SHEET 1 AA3 3 GLN A 238 SER A 239 0
SHEET 2 AA3 3 ILE A 282 LEU A 284 -1 O LEU A 284 N GLN A 238
SHEET 3 AA3 3 LEU A 289 LEU A 291 -1 O LYS A 290 N MET A 283
SHEET 1 AA4 2 LEU A 272 VAL A 273 0
SHEET 2 AA4 2 SER A 298 ARG A 299 -1 O SER A 298 N VAL A 273
SHEET 1 AA5 2 THR A 344 ARG A 345 0
SHEET 2 AA5 2 ARG A 348 TYR A 349 -1 O ARG A 348 N ARG A 345
LINK SG CYS A 106 ZN ZN A 502 1555 1555 2.45
LINK SG CYS A 109 ZN ZN A 502 1555 1555 2.44
LINK SG CYS A 128 ZN ZN A 502 1555 1555 2.23
LINK SG CYS A 131 ZN ZN A 502 1555 1555 2.34
LINK OD1 ASN A 281 MG MG A 503 1555 1555 2.42
LINK OD2 ASP A 293 MG MG A 503 1555 1555 2.26
LINK OD1 ASP A 293 MG MG A 504 1555 1555 2.39
LINK OD2 ASP A 293 MG MG A 504 1555 1555 2.84
LINK O3B AGS A 501 MG MG A 503 1555 1555 2.89
LINK O2A AGS A 501 MG MG A 503 1555 1555 2.20
LINK O2G AGS A 501 MG MG A 504 1555 1555 2.03
LINK MG MG A 503 O HOH A 607 1555 1555 2.16
LINK MG MG A 503 O HOH A 628 1555 1555 2.35
LINK MG MG A 504 O HOH A 602 1555 1555 2.45
LINK MG MG A 504 O HOH A 612 1555 1555 2.59
LINK MG MG A 504 O HOH A 629 1555 1555 2.17
LINK MG MG A 504 O HOH A 693 1555 1555 2.63
SITE 1 AC1 21 ARG A 83 ASP A 86 GLY A 160 GLY A 161
SITE 2 AC1 21 LEU A 162 VAL A 179 LYS A 181 MET A 232
SITE 3 AC1 21 GLU A 233 TYR A 234 VAL A 235 ASN A 281
SITE 4 AC1 21 ASP A 293 MG A 503 MG A 504 HOH A 602
SITE 5 AC1 21 HOH A 608 HOH A 667 HOH A 676 HOH A 687
SITE 6 AC1 21 HOH A 693
SITE 1 AC2 4 CYS A 106 CYS A 109 CYS A 128 CYS A 131
SITE 1 AC3 5 ASN A 281 ASP A 293 AGS A 501 HOH A 607
SITE 2 AC3 5 HOH A 628
SITE 1 AC4 6 ASP A 293 AGS A 501 HOH A 602 HOH A 612
SITE 2 AC4 6 HOH A 629 HOH A 693
CRYST1 75.452 37.183 108.032 90.00 97.93 90.00 C 1 2 1 4
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 0.013253 0.000000 0.001846 0.00000
SCALE2 0.000000 0.026894 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009346 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
