HEADER TRANSFERASE 29-SEP-15 5E0Z TITLE CRYSTAL STRUCTURE OF PASTA DOMAINS 3 AND 4 OF MYCOBACTERIUM TITLE 2 TUBERCULOSIS PROTEIN KINASE B COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PKNB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 491-626; 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 STRAIN: ATCC 25618 / H37RV; SOURCE 6 GENE: PKNB, RV0014C, MTCY10H4.14C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, EXTRACELLULAR SENSOR DOMAIN, PEPTIDOGLYCAN BINDING, KEYWDS 2 STRUCTURAL GENOMICS, TB STRUCTURAL GENOMICS CONSORTIUM, TBSGC, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.M.PRIGOZHIN,TB STRUCTURAL GENOMICS CONSORTIUM (TBSGC) REVDAT 6 06-MAR-24 5E0Z 1 REMARK REVDAT 5 25-DEC-19 5E0Z 1 REMARK REVDAT 4 13-SEP-17 5E0Z 1 JRNL REMARK REVDAT 3 09-NOV-16 5E0Z 1 JRNL REVDAT 2 21-SEP-16 5E0Z 1 JRNL REVDAT 1 14-SEP-16 5E0Z 0 JRNL AUTH D.M.PRIGOZHIN,K.G.PAPAVINASASUNDARAM,C.E.BAER,K.C.MURPHY, JRNL AUTH 2 A.MOSKALEVA,T.Y.CHEN,T.ALBER,C.M.SASSETTI JRNL TITL STRUCTURAL AND GENETIC ANALYSES OF THE MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS PROTEIN KINASE B SENSOR DOMAIN IDENTIFY A JRNL TITL 3 POTENTIAL LIGAND-BINDING SITE. JRNL REF J.BIOL.CHEM. V. 291 22961 2016 JRNL REFN ESSN 1083-351X JRNL PMID 27601474 JRNL DOI 10.1074/JBC.M116.731760 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 8126 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 809 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.9569 - 3.6327 0.98 1357 152 0.1652 0.1881 REMARK 3 2 3.6327 - 2.8836 0.97 1282 143 0.1705 0.2104 REMARK 3 3 2.8836 - 2.5192 0.96 1266 141 0.2143 0.2802 REMARK 3 4 2.5192 - 2.2889 0.92 1203 134 0.2204 0.2646 REMARK 3 5 2.2889 - 2.1248 0.89 1168 128 0.2280 0.2690 REMARK 3 6 2.1248 - 1.9996 0.80 1041 111 0.2343 0.2959 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 1049 REMARK 3 ANGLE : 0.772 1434 REMARK 3 CHIRALITY : 0.023 158 REMARK 3 PLANARITY : 0.003 197 REMARK 3 DIHEDRAL : 12.428 384 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5E0Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000214033. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.116 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8592 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 39.949 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 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) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.47900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.2.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 4.5, 2M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 12.27250 REMARK 290 SMTRY3 2 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OUV RELATED DB: PDB REMARK 900 RELATED ID: 5E0Y RELATED DB: PDB REMARK 900 RELATED ID: 5E10 RELATED DB: PDB REMARK 900 RELATED ID: 5E12 RELATED DB: PDB DBREF 5E0Z A 491 626 UNP P9WI81 PKNB_MYCTU 491 626 SEQRES 1 A 136 GLY PRO ALA THR LYS ASP ILE PRO ASP VAL ALA GLY GLN SEQRES 2 A 136 THR VAL ASP VAL ALA GLN LYS ASN LEU ASN VAL TYR GLY SEQRES 3 A 136 PHE THR LYS PHE SER GLN ALA SER VAL ASP SER PRO ARG SEQRES 4 A 136 PRO ALA GLY GLU VAL THR GLY THR ASN PRO PRO ALA GLY SEQRES 5 A 136 THR THR VAL PRO VAL ASP SER VAL ILE GLU LEU GLN VAL SEQRES 6 A 136 SER LYS GLY ASN GLN PHE VAL MET PRO ASP LEU SER GLY SEQRES 7 A 136 MET PHE TRP VAL ASP ALA GLU PRO ARG LEU ARG ALA LEU SEQRES 8 A 136 GLY TRP THR GLY MET LEU ASP LYS GLY ALA ASP VAL ASP SEQRES 9 A 136 ALA GLY GLY SER GLN HIS ASN ARG VAL VAL TYR GLN ASN SEQRES 10 A 136 PRO PRO ALA GLY THR GLY VAL ASN ARG ASP GLY ILE ILE SEQRES 11 A 136 THR LEU ARG PHE GLY GLN FORMUL 2 HOH *100(H2 O) HELIX 1 AA1 THR A 504 GLY A 516 1 13 HELIX 2 AA2 PHE A 570 ALA A 580 1 11 HELIX 3 AA3 GLY A 596 HIS A 600 5 5 SHEET 1 AA1 2 THR A 494 ASP A 496 0 SHEET 2 AA1 2 THR A 544 PRO A 546 -1 O VAL A 545 N LYS A 495 SHEET 1 AA2 3 PHE A 520 VAL A 525 0 SHEET 2 AA2 3 ILE A 551 SER A 556 1 O VAL A 555 N ALA A 523 SHEET 3 AA2 3 VAL A 534 ASN A 538 -1 N THR A 535 O GLN A 554 SHEET 1 AA3 2 GLN A 560 VAL A 562 0 SHEET 2 AA3 2 GLY A 613 ASN A 615 -1 O VAL A 614 N PHE A 561 SHEET 1 AA4 3 LEU A 587 LYS A 589 0 SHEET 2 AA4 3 ILE A 620 PHE A 624 1 O ILE A 620 N ASP A 588 SHEET 3 AA4 3 VAL A 603 ASN A 607 -1 N ASN A 607 O THR A 621 CISPEP 1 ASN A 538 PRO A 539 0 0.34 CISPEP 2 ASN A 607 PRO A 608 0 1.44 CRYST1 40.466 24.545 64.874 90.00 99.17 90.00 P 1 21 1 2 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 0.024712 0.000000 0.003989 0.00000 SCALE2 0.000000 0.040741 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015614 0.00000