HEADER TRANSFERASE 27-FEB-12 4DXL TITLE CRYSTAL STRUCTURE OF ISPE (4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL TITLE 2 KINASE) FROM MYCOBACTERIUM ABSCESSUS, BOUND TO CMP AND 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 4 13-SEP-23 4DXL 1 REMARK SEQADV REVDAT 3 22-APR-15 4DXL 1 JRNL REVDAT 2 11-APR-12 4DXL 1 JRNL REVDAT 1 07-MAR-12 4DXL 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 17719 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 905 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1125 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.1630 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.2010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2180 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 215 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : 0.73000 REMARK 3 B33 (A**2) : -0.50000 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): 0.241 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.203 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.914 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.838 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2299 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1435 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3161 ; 1.567 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3507 ; 0.923 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 311 ; 6.932 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;36.996 ;23.978 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 309 ;12.810 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;17.848 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 371 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2652 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 464 ; 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 : 6 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 5 A 61 REMARK 3 ORIGIN FOR THE GROUP (A): -6.2050 15.0850 -1.4170 REMARK 3 T TENSOR REMARK 3 T11: 0.0552 T22: 0.0144 REMARK 3 T33: 0.0556 T12: 0.0258 REMARK 3 T13: 0.0138 T23: 0.0096 REMARK 3 L TENSOR REMARK 3 L11: 0.4535 L22: 0.2998 REMARK 3 L33: 2.3855 L12: 0.0570 REMARK 3 L13: 0.4902 L23: 0.1670 REMARK 3 S TENSOR REMARK 3 S11: -0.0308 S12: -0.0227 S13: -0.0242 REMARK 3 S21: 0.0532 S22: 0.0407 S23: 0.0311 REMARK 3 S31: 0.0751 S32: 0.0629 S33: -0.0099 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 62 A 75 REMARK 3 ORIGIN FOR THE GROUP (A): -7.4420 28.8720 5.1030 REMARK 3 T TENSOR REMARK 3 T11: 0.1527 T22: 0.0385 REMARK 3 T33: 0.0578 T12: 0.0055 REMARK 3 T13: -0.0212 T23: -0.0327 REMARK 3 L TENSOR REMARK 3 L11: 14.1001 L22: 0.8083 REMARK 3 L33: 7.5463 L12: 2.5302 REMARK 3 L13: -10.1738 L23: -2.0950 REMARK 3 S TENSOR REMARK 3 S11: 0.1111 S12: 0.1258 S13: 0.2918 REMARK 3 S21: 0.1689 S22: 0.0775 S23: 0.0218 REMARK 3 S31: -0.2019 S32: -0.1380 S33: -0.1887 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 76 A 180 REMARK 3 ORIGIN FOR THE GROUP (A): -6.8260 12.2140 1.7550 REMARK 3 T TENSOR REMARK 3 T11: 0.0617 T22: 0.0220 REMARK 3 T33: 0.0357 T12: 0.0165 REMARK 3 T13: 0.0057 T23: 0.0108 REMARK 3 L TENSOR REMARK 3 L11: 0.1624 L22: 0.7528 REMARK 3 L33: 1.4123 L12: -0.0875 REMARK 3 L13: -0.0210 L23: 0.3662 REMARK 3 S TENSOR REMARK 3 S11: -0.0341 S12: -0.0450 S13: -0.0077 REMARK 3 S21: 0.0862 S22: 0.0007 S23: 0.0648 REMARK 3 S31: 0.1601 S32: -0.0320 S33: 0.0334 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 181 A 206 REMARK 3 ORIGIN FOR THE GROUP (A): -19.5010 21.5670 -17.0180 REMARK 3 T TENSOR REMARK 3 T11: 0.0510 T22: 0.0439 REMARK 3 T33: 0.0727 T12: 0.0284 REMARK 3 T13: -0.0040 T23: 0.0214 REMARK 3 L TENSOR REMARK 3 L11: 3.2746 L22: 1.2531 REMARK 3 L33: 1.9011 L12: 1.1065 REMARK 3 L13: 0.9629 L23: 0.7336 REMARK 3 S TENSOR REMARK 3 S11: 0.0789 S12: 0.0462 S13: 0.1381 REMARK 3 S21: 0.0104 S22: -0.0593 S23: 0.1596 REMARK 3 S31: -0.1294 S32: -0.2268 S33: -0.0196 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 207 A 229 REMARK 3 ORIGIN FOR THE GROUP (A): -2.7140 7.8040 -24.4690 REMARK 3 T TENSOR REMARK 3 T11: 0.0982 T22: 0.0130 REMARK 3 T33: 0.1018 T12: 0.0120 REMARK 3 T13: -0.0068 T23: -0.0253 REMARK 3 L TENSOR REMARK 3 L11: 2.0358 L22: 1.9579 REMARK 3 L33: 1.7670 L12: -0.3720 REMARK 3 L13: 1.8837 L23: -0.4807 REMARK 3 S TENSOR REMARK 3 S11: 0.0136 S12: 0.1079 S13: -0.0933 REMARK 3 S21: -0.2003 S22: 0.0258 S23: -0.0059 REMARK 3 S31: 0.0127 S32: 0.0890 S33: -0.0394 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 230 A 308 REMARK 3 ORIGIN FOR THE GROUP (A): -2.2330 23.8930 -17.3600 REMARK 3 T TENSOR REMARK 3 T11: 0.0519 T22: 0.0180 REMARK 3 T33: 0.0583 T12: -0.0017 REMARK 3 T13: 0.0020 T23: 0.0138 REMARK 3 L TENSOR REMARK 3 L11: 0.4206 L22: 0.4466 REMARK 3 L33: 1.1091 L12: -0.0451 REMARK 3 L13: -0.0897 L23: 0.0802 REMARK 3 S TENSOR REMARK 3 S11: -0.0373 S12: 0.0415 S13: 0.0995 REMARK 3 S21: -0.0174 S22: 0.0175 S23: -0.0354 REMARK 3 S31: -0.0889 S32: 0.0828 S33: 0.0198 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 4DXL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070909. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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 : 17719 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.19200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.400 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 3PYG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: INTERNAL TRACKING NUMBER 230819A2, REMARK 280 INDEX SCREEN CONDITION A2: 2 M AMMONIUM SULFATE, 0.1 M ACETATE, REMARK 280 PH 4.5, MYABA.00725.A.A1 PW30213 AT 29.3 MG/ML IN 25 MM HEPES, REMARK 280 PH 7.0, 500 MM SODIUM CHLORIDE, 2 MM DTT, 0.025% SODIUM AZIDE, 5% REMARK 280 GLYCEROL, 2 MM CDP, 2 MM ATP, 2 MM MESO-ERYTHRITOL, REMARK 280 CRYOPROTECTANT: AL'S OIL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 23.29500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.04500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.29500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.04500 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 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 553 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 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 VAL A 5 CG1 CG2 REMARK 470 ASP A 33 CG OD1 OD2 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 250 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 GLU A 76 NE2 GLN A 82 1.99 REMARK 500 OD2 ASP A 278 O HOH A 673 2.08 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 0.061 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. = 3.1 DEGREES REMARK 500 ARG A 225 NE - CZ - NH2 ANGL. DEV. = -3.2 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 34 1.15 -51.48 REMARK 500 SER A 47 1.01 -68.15 REMARK 500 THR A 71 -51.51 -122.96 REMARK 500 ASP A 75 -157.77 -104.01 REMARK 500 ASP A 204 73.59 -117.53 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 GLY A 70 THR A 71 -137.18 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 C5P A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SSGCID-MYABA.00725.A RELATED DB: TARGETTRACK DBREF 4DXL A 1 314 UNP B1MKD5 B1MKD5_MYCA9 1 314 SEQADV 4DXL GLY A -3 UNP B1MKD5 EXPRESSION TAG SEQADV 4DXL PRO A -2 UNP B1MKD5 EXPRESSION TAG SEQADV 4DXL GLY A -1 UNP B1MKD5 EXPRESSION TAG SEQADV 4DXL 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 C5P A 401 21 HET ATP A 402 31 HET CL A 403 1 HETNAM C5P CYTIDINE-5'-MONOPHOSPHATE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM CL CHLORIDE ION FORMUL 2 C5P C9 H14 N3 O8 P FORMUL 3 ATP C10 H16 N5 O13 P3 FORMUL 4 CL CL 1- FORMUL 5 HOH *215(H2 O) HELIX 1 1 ASN A 78 GLY A 92 1 15 HELIX 2 2 ALA A 112 HIS A 130 1 19 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 GLY A 288 1 14 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 HIS A 37 ASP A 56 -1 N ASP A 51 O ASN A 102 SHEET 4 A 5 VAL A 14 LEU A 31 -1 N VAL A 16 O VAL A 52 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 HIS A 37 ASP A 56 -1 N PHE A 43 O ALA A 158 SHEET 4 B 5 VAL A 14 LEU A 31 -1 N VAL A 16 O VAL A 52 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 3.85 CISPEP 2 GLY A 300 PRO A 301 0 3.68 SITE 1 AC1 9 TYR A 36 HIS A 37 LEU A 39 SER A 147 SITE 2 AC1 9 ARG A 163 THR A 189 PHE A 193 HOH A 604 SITE 3 AC1 9 HOH A 641 SITE 1 AC2 24 PRO A 73 ARG A 77 ASN A 78 LEU A 79 SITE 2 AC2 24 LYS A 103 VAL A 107 ALA A 108 GLY A 109 SITE 3 AC2 24 GLY A 110 ALA A 112 GLY A 113 GLY A 114 SITE 4 AC2 24 ASP A 117 ASP A 148 THR A 189 HOH A 503 SITE 5 AC2 24 HOH A 507 HOH A 518 HOH A 528 HOH A 652 SITE 6 AC2 24 HOH A 674 HOH A 675 HOH A 702 HOH A 709 SITE 1 AC3 1 HIS A 154 CRYST1 46.590 110.090 53.290 90.00 90.00 90.00 P 21 21 2 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 0.021464 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018765 0.00000