HEADER TRANSFERASE 29-SEP-15 5E10 TITLE CRYSTAL STRUCTURE OF PASTA DOMAINS 1 AND 2 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 360-491; 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 5E10 1 REMARK REVDAT 5 25-DEC-19 5E10 1 REMARK REVDAT 4 13-SEP-17 5E10 1 JRNL REMARK REVDAT 3 09-NOV-16 5E10 1 JRNL REVDAT 2 21-SEP-16 5E10 1 JRNL REVDAT 1 14-SEP-16 5E10 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 13498 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 673 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 42.0062 - 3.0794 1.00 2619 137 0.1624 0.1949 REMARK 3 2 3.0794 - 2.4443 1.00 2573 135 0.1722 0.1942 REMARK 3 3 2.4443 - 2.1353 1.00 2577 135 0.1606 0.2092 REMARK 3 4 2.1353 - 1.9401 1.00 2545 134 0.1744 0.2376 REMARK 3 5 1.9401 - 1.8010 0.99 2511 132 0.2095 0.2640 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.92 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 : 0.008 1052 REMARK 3 ANGLE : 1.212 1454 REMARK 3 CHIRALITY : 0.049 175 REMARK 3 PLANARITY : 0.006 202 REMARK 3 DIHEDRAL : 13.178 393 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 5E10 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_1000214034. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-AUG-11 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 : 13502 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 41.995 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.57100 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CHES PH 9.5, 30% ISOPROPANOL, REMARK 280 30% PEG 3350, VAPOR DIFFUSION, 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 40.36050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.58150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.36050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.58150 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7400 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 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 631 LIES ON A SPECIAL POSITION. 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 HOH A 505 O HOH A 615 2.08 REMARK 500 O HOH A 570 O HOH A 630 2.08 REMARK 500 O HOH A 533 O HOH A 574 2.15 REMARK 500 OE1 GLN A 454 O HOH A 501 2.19 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 ASN A 407 -5.55 74.83 REMARK 500 THR A 434 -4.19 67.74 REMARK 500 ASN A 475 -3.67 72.97 REMARK 500 REMARK 500 REMARK: NULL 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: 5E0Z RELATED DB: PDB REMARK 900 RELATED ID: 5E12 RELATED DB: PDB DBREF 5E10 A 360 491 UNP P9WI81 PKNB_MYCTU 360 491 SEQADV 5E10 GLY A 359 UNP P9WI81 EXPRESSION TAG SEQRES 1 A 133 GLY VAL GLN VAL PRO ASP VAL ARG GLY GLN SER SER ALA SEQRES 2 A 133 ASP ALA ILE ALA THR LEU GLN ASN ARG GLY PHE LYS ILE SEQRES 3 A 133 ARG THR LEU GLN LYS PRO ASP SER THR ILE PRO PRO ASP SEQRES 4 A 133 HIS VAL ILE GLY THR ASP PRO ALA ALA ASN THR SER VAL SEQRES 5 A 133 SER ALA GLY ASP GLU ILE THR VAL ASN VAL SER THR GLY SEQRES 6 A 133 PRO GLU GLN ARG GLU ILE PRO ASP VAL SER THR LEU THR SEQRES 7 A 133 TYR ALA GLU ALA VAL LYS LYS LEU THR ALA ALA GLY PHE SEQRES 8 A 133 GLY ARG PHE LYS GLN ALA ASN SER PRO SER THR PRO GLU SEQRES 9 A 133 LEU VAL GLY LYS VAL ILE GLY THR ASN PRO PRO ALA ASN SEQRES 10 A 133 GLN THR SER ALA ILE THR ASN VAL VAL ILE ILE ILE VAL SEQRES 11 A 133 GLY SER GLY FORMUL 2 HOH *135(H2 O) HELIX 1 AA1 SER A 369 ARG A 380 1 12 HELIX 2 AA2 THR A 436 ALA A 447 1 12 HELIX 3 AA3 THR A 460 VAL A 464 5 5 SHEET 1 AA1 2 VAL A 360 GLN A 361 0 SHEET 2 AA1 2 SER A 409 VAL A 410 -1 O VAL A 410 N VAL A 360 SHEET 1 AA2 3 LYS A 383 LYS A 389 0 SHEET 2 AA2 3 GLU A 415 SER A 421 1 O VAL A 420 N LEU A 387 SHEET 3 AA2 3 VAL A 399 ASP A 403 -1 N ILE A 400 O ASN A 419 SHEET 1 AA3 2 GLN A 426 GLU A 428 0 SHEET 2 AA3 2 THR A 477 ALA A 479 -1 O SER A 478 N ARG A 427 SHEET 1 AA4 3 PHE A 452 PRO A 458 0 SHEET 2 AA4 3 VAL A 484 SER A 490 1 O VAL A 488 N ALA A 455 SHEET 3 AA4 3 VAL A 467 ASN A 471 -1 N ASN A 471 O ILE A 485 CISPEP 1 ASP A 403 PRO A 404 0 0.88 CISPEP 2 ASP A 403 PRO A 404 0 -2.42 CISPEP 3 ASN A 471 PRO A 472 0 7.17 CRYST1 80.721 43.163 43.749 90.00 106.28 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 0.012388 0.000000 0.003618 0.00000 SCALE2 0.000000 0.023168 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023812 0.00000