HEADER TRANSFERASE 26-MAR-12 4ED4 TITLE CRYSTAL STRUCTURE OF ISPE (4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL TITLE 2 KINASE) FROM MYCOBACTERIUM ABCESSUS, BOUND TO ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ISPE, CMK, 4-(CYTIDINE-5'-DIPHOSPHO)-2-C-METHYL-D-ERYTHRITOL COMPND 5 KINASE; COMPND 6 EC: 2.7.1.148; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM ABSCESSUS; SOURCE 3 ORGANISM_TAXID: 561007; SOURCE 4 STRAIN: ATCC 19977 / DSM 44196; SOURCE 5 GENE: ISPE, MAB_1139; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: AVA0421 KEYWDS SSGCID, NIH, NIAID, SBRI, EMERALD BIOSTRUCTURES, STRUCTURAL GENOMICS, KEYWDS 2 SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 3 13-SEP-23 4ED4 1 REMARK SEQADV REVDAT 2 22-APR-15 4ED4 1 JRNL REVDAT 1 04-APR-12 4ED4 0 JRNL AUTH L.BAUGH,I.PHAN,D.W.BEGLEY,M.C.CLIFTON,B.ARMOUR,D.M.DRANOW, JRNL AUTH 2 B.M.TAYLOR,M.M.MURUTHI,J.ABENDROTH,J.W.FAIRMAN,D.FOX, JRNL AUTH 3 S.H.DIETERICH,B.L.STAKER,A.S.GARDBERG,R.CHOI,S.N.HEWITT, JRNL AUTH 4 A.J.NAPULI,J.MYERS,L.K.BARRETT,Y.ZHANG,M.FERRELL,E.MUNDT, JRNL AUTH 5 K.THOMPKINS,N.TRAN,S.LYONS-ABBOTT,A.ABRAMOV,A.SEKAR, JRNL AUTH 6 D.SERBZHINSKIY,D.LORIMER,G.W.BUCHKO,R.STACY,L.J.STEWART, JRNL AUTH 7 T.E.EDWARDS,W.C.VAN VOORHIS,P.J.MYLER JRNL TITL INCREASING THE STRUCTURAL COVERAGE OF TUBERCULOSIS DRUG JRNL TITL 2 TARGETS. JRNL REF TUBERCULOSIS (EDINB) V. 95 142 2015 JRNL REFN ISSN 1472-9792 JRNL PMID 25613812 JRNL DOI 10.1016/J.TUBE.2014.12.003 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 26898 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1370 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1516 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.1650 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.2400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2134 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 245 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : 0.34000 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): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.063 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.522 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2241 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1400 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3081 ; 1.535 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3429 ; 0.864 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 309 ; 7.133 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;34.926 ;24.111 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 305 ;11.958 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;15.520 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 364 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2596 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 446 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 308 REMARK 3 ORIGIN FOR THE GROUP (A): -16.8510 7.1300 -16.8210 REMARK 3 T TENSOR REMARK 3 T11: 0.0314 T22: 0.0268 REMARK 3 T33: 0.0094 T12: 0.0056 REMARK 3 T13: 0.0116 T23: 0.0129 REMARK 3 L TENSOR REMARK 3 L11: 0.2588 L22: 1.2745 REMARK 3 L33: 0.4119 L12: -0.1651 REMARK 3 L13: -0.1827 L23: 0.1912 REMARK 3 S TENSOR REMARK 3 S11: -0.0557 S12: 0.0003 S13: -0.0221 REMARK 3 S21: 0.0565 S22: 0.0202 S23: 0.0446 REMARK 3 S31: 0.0679 S32: 0.0385 S33: 0.0355 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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: U VALUES : WITH TLS ADDED REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 4ED4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071466. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541780 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26899 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 42.738 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.85 REMARK 200 R MERGE FOR SHELL (I) : 0.14300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.80 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: PDB ENTRY 4DXL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: INTERNAL TRACKING NUMBER 231560F1, REMARK 280 CSHT SCREEN CONDITION F1: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE, PH 4.6, 30% PEG2000 MME, MYABA.00725.A.A1 REMARK 280 PW30213 AT 29.3 MG/ML IN 25 MM HEPES, PH 7.0, 500 MM SODIUM REMARK 280 CHLORIDE, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 2 MM ATP, REMARK 280 2 MM EBSI1799, CRYOPROTECTANT: AL'S OIL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 23.22500 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.55500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 23.22500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.55500 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 556 LIES ON A SPECIAL POSITION. 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 GLY A -3 REMARK 465 PRO A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 GLU A 3 REMARK 465 THR A 4 REMARK 465 VAL A 5 REMARK 465 ARG A 32 REMARK 465 ASP A 33 REMARK 465 ASP A 34 REMARK 465 GLY A 35 REMARK 465 GLN A 309 REMARK 465 GLY A 310 REMARK 465 ARG A 311 REMARK 465 SER A 312 REMARK 465 ASP A 313 REMARK 465 GLY A 314 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 ASP A 7 CG OD1 OD2 REMARK 470 LEU A 31 CG CD1 CD2 REMARK 470 TYR A 36 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 135 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 136 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 194 CG CD CE NZ REMARK 470 ASP A 204 CG OD1 OD2 REMARK 470 ARG A 246 CG CD NE CZ NH1 NH2 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 O TRP A 8 OG1 THR A 15 2.15 REMARK 500 NH2 ARG A 55 O HOH A 721 2.19 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 HIS A 139 CG HIS A 139 CD2 0.057 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 225 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 225 NE - CZ - NH2 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 ASP A 75 -156.66 -107.49 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 ASP A 30 LEU A 31 134.12 REMARK 500 GLY A 70 THR A 71 -147.73 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 ATP A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DXL RELATED DB: PDB REMARK 900 WITH ATP AND CMP BOUND REMARK 900 RELATED ID: SSGCID-MYABA.00725.A RELATED DB: TARGETTRACK DBREF 4ED4 A 1 314 UNP B1MKD5 B1MKD5_MYCA9 1 314 SEQADV 4ED4 GLY A -3 UNP B1MKD5 EXPRESSION TAG SEQADV 4ED4 PRO A -2 UNP B1MKD5 EXPRESSION TAG SEQADV 4ED4 GLY A -1 UNP B1MKD5 EXPRESSION TAG SEQADV 4ED4 SER A 0 UNP B1MKD5 EXPRESSION TAG SEQRES 1 A 318 GLY PRO GLY SER MET SER GLU THR VAL SER ASP TRP VAL SEQRES 2 A 318 PRO THR GLY ALA VAL THR VAL ARG ALA PRO GLY LYS VAL SEQRES 3 A 318 ASN LEU TYR LEU ALA VAL GLY ASP LEU ARG ASP ASP GLY SEQRES 4 A 318 TYR HIS GLU LEU THR THR VAL PHE HIS ALA VAL SER LEU SEQRES 5 A 318 ALA ASP ASP VAL THR VAL ARG ASP ALA ASP VAL LEU SER SEQRES 6 A 318 ILE ASP VAL VAL GLY GLN GLY GLU GLY THR VAL PRO THR SEQRES 7 A 318 ASP GLU ARG ASN LEU ALA TRP GLN ALA ALA GLU LEU PHE SEQRES 8 A 318 ALA ASP HIS VAL GLY ARG ALA PRO ASP VAL SER ILE PHE SEQRES 9 A 318 ILE ASN LYS ASP ILE PRO VAL ALA GLY GLY MET ALA GLY SEQRES 10 A 318 GLY SER ALA ASP ALA ALA ALA VAL LEU VAL ALA MET ASN SEQRES 11 A 318 GLU LEU TRP HIS ALA GLY VAL PRO ARG ARG ASP LEU HIS SEQRES 12 A 318 HIS LEU ALA ALA GLN LEU GLY SER ASP VAL PRO PHE ALA SEQRES 13 A 318 LEU HIS GLY GLY THR ALA LEU GLY THR GLY ARG GLY GLU SEQRES 14 A 318 GLN LEU ALA THR VAL LEU ALA ARG ASN VAL PHE HIS TRP SEQRES 15 A 318 VAL PHE ALA PHE ALA ASP GLY GLY LEU ALA THR PRO GLN SEQRES 16 A 318 VAL PHE LYS GLU ILE ASP ARG LEU ARG GLU ASN GLY ASP SEQRES 17 A 318 PRO PRO ARG LEU ALA GLU ALA ASP GLU LEU LEU GLY ALA SEQRES 18 A 318 LEU ALA ALA GLY ASP ALA ARG ARG LEU ALA PRO LEU LEU SEQRES 19 A 318 GLY ASN GLU LEU GLN ALA ALA ALA VAL SER LEU ASN PRO SEQRES 20 A 318 GLU LEU ARG ARG THR LEU ARG ALA GLY GLU SER ALA GLY SEQRES 21 A 318 ALA LEU ALA GLY ILE VAL SER GLY SER GLY PRO THR CYS SEQRES 22 A 318 ALA PHE LEU CYS THR SER ALA ASP ASP ALA VAL GLN VAL SEQRES 23 A 318 SER ALA GLU LEU ALA GLY ALA GLY VAL CYS ARG THR VAL SEQRES 24 A 318 ARG VAL ALA SER GLY PRO VAL HIS GLY ALA GLN VAL ILE SEQRES 25 A 318 GLN GLY ARG SER ASP GLY HET ATP A 401 31 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 HOH *245(H2 O) HELIX 1 1 ASN A 78 VAL A 91 1 14 HELIX 2 2 ALA A 112 TRP A 129 1 18 HELIX 3 3 PRO A 134 GLY A 146 1 13 HELIX 4 4 ASP A 148 GLY A 155 1 8 HELIX 5 5 ALA A 188 GLY A 203 1 16 HELIX 6 6 ALA A 211 GLY A 221 1 11 HELIX 7 7 ASP A 222 ALA A 227 1 6 HELIX 8 8 PRO A 228 LEU A 230 5 3 HELIX 9 9 LEU A 234 ASN A 242 1 9 HELIX 10 10 GLU A 244 ALA A 255 1 12 HELIX 11 11 SER A 275 ALA A 289 1 15 SHEET 1 A 5 SER A 61 GLY A 66 0 SHEET 2 A 5 VAL A 97 LYS A 103 1 O ILE A 101 N ASP A 63 SHEET 3 A 5 LEU A 39 ASP A 56 -1 N ASP A 51 O ASN A 102 SHEET 4 A 5 VAL A 14 VAL A 28 -1 N VAL A 14 O VAL A 54 SHEET 5 A 5 GLY A 231 ASN A 232 1 O GLY A 231 N LEU A 24 SHEET 1 B 5 GLN A 166 THR A 169 0 SHEET 2 B 5 THR A 157 THR A 161 -1 N LEU A 159 O ALA A 168 SHEET 3 B 5 LEU A 39 ASP A 56 -1 N THR A 41 O GLY A 160 SHEET 4 B 5 VAL A 14 VAL A 28 -1 N VAL A 14 O VAL A 54 SHEET 5 B 5 GLN A 306 VAL A 307 -1 O GLN A 306 N ARG A 17 SHEET 1 C 4 ALA A 259 VAL A 262 0 SHEET 2 C 4 CYS A 269 CYS A 273 -1 O ALA A 270 N ILE A 261 SHEET 3 C 4 PHE A 176 PHE A 182 -1 N HIS A 177 O CYS A 273 SHEET 4 C 4 THR A 294 GLY A 300 -1 O GLY A 300 N PHE A 176 CISPEP 1 GLY A 266 PRO A 267 0 3.84 CISPEP 2 GLY A 300 PRO A 301 0 3.83 SITE 1 AC1 28 PRO A 73 ARG A 77 ASN A 78 LEU A 79 SITE 2 AC1 28 LYS A 103 VAL A 107 ALA A 108 GLY A 109 SITE 3 AC1 28 GLY A 110 MET A 111 ALA A 112 GLY A 113 SITE 4 AC1 28 GLY A 114 ASP A 117 ASP A 148 THR A 189 SITE 5 AC1 28 HOH A 508 HOH A 514 HOH A 516 HOH A 518 SITE 6 AC1 28 HOH A 520 HOH A 536 HOH A 560 HOH A 568 SITE 7 AC1 28 HOH A 574 HOH A 623 HOH A 655 HOH A 683 CRYST1 46.450 53.360 109.110 90.00 90.00 90.00 P 21 2 21 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 0.021529 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018741 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009165 0.00000