HEADER TRANSFERASE 23-APR-12 4ESQ TITLE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF PKNH FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE PROTEIN KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 83332-83523; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: PKNH, RV1266C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODONPLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS RECEPTOR KINASE, MEMBRANE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CAVAZOS,D.M.PRIGOZHIN,T.ALBER REVDAT 3 15-NOV-17 4ESQ 1 REMARK REVDAT 2 02-JAN-13 4ESQ 1 JRNL REVDAT 1 18-JUL-12 4ESQ 0 JRNL AUTH A.CAVAZOS,D.M.PRIGOZHIN,T.ALBER JRNL TITL STRUCTURE OF THE SENSOR DOMAIN OF MYCOBACTERIUM TUBERCULOSIS JRNL TITL 2 PKNH RECEPTOR KINASE REVEALS A CONSERVED BINDING CLEFT. JRNL REF J.MOL.BIOL. V. 422 488 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22727744 JRNL DOI 10.1016/J.JMB.2012.06.011 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.1_743 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 34190 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 878 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 48.8042 - 3.8925 0.99 2770 147 0.1461 0.1787 REMARK 3 2 3.8925 - 3.0897 0.98 2775 133 0.1538 0.1721 REMARK 3 3 3.0897 - 2.6992 0.98 2755 144 0.1739 0.1899 REMARK 3 4 2.6992 - 2.4524 0.98 2756 142 0.1781 0.2281 REMARK 3 5 2.4524 - 2.2767 0.98 2720 133 0.1703 0.1967 REMARK 3 6 2.2767 - 2.1424 0.97 2735 145 0.1523 0.2173 REMARK 3 7 2.1424 - 2.0351 0.96 2707 141 0.1512 0.1730 REMARK 3 8 2.0351 - 1.9465 0.96 2710 144 0.1531 0.2132 REMARK 3 9 1.9465 - 1.8716 0.96 2663 148 0.1635 0.2169 REMARK 3 10 1.8716 - 1.8070 0.96 2686 122 0.1842 0.2165 REMARK 3 11 1.8070 - 1.7505 0.94 2635 147 0.1985 0.2681 REMARK 3 12 1.7505 - 1.7005 0.94 2595 137 0.2261 0.2368 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 28.93 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.70310 REMARK 3 B22 (A**2) : -0.80740 REMARK 3 B33 (A**2) : 2.51050 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.69780 REMARK 3 B23 (A**2) : 0.00000 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 : 0.013 1522 REMARK 3 ANGLE : 0.960 2084 REMARK 3 CHIRALITY : 0.060 236 REMARK 3 PLANARITY : 0.004 270 REMARK 3 DIHEDRAL : 18.747 556 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 4ESQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000072022. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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) : 1.1159 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34200 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.25300 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: SAD REMARK 200 SOFTWARE USED: SOLVE 2.13, RESOLVE 2.15 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, 0.2 M AMMONIUM REMARK 280 ACETATE, 25% PEG 3350, 50MM TERBIUM NITRATE, PH 5.5, VAPOR REMARK 280 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 17.96150 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 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 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 943 O HOH A 991 2.09 REMARK 500 O THR A 549 O HOH A 982 2.15 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 LYS A 567 -165.49 -122.75 REMARK 500 ASN A 595 -132.69 53.59 REMARK 500 THR A 609 -63.69 -129.15 REMARK 500 ASN A 610 30.46 -143.48 REMARK 500 REMARK 500 REMARK: NULL 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 TB A 702 TB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BTB A 701 O1 REMARK 620 2 BTB A 701 O8 104.8 REMARK 620 3 HOH A1017 O 68.6 146.1 REMARK 620 4 BTB A 701 O6 123.8 83.0 129.1 REMARK 620 5 HOH A1008 O 71.9 68.3 78.3 150.7 REMARK 620 6 BTB A 701 N 70.9 75.1 128.2 57.4 117.6 REMARK 620 7 HOH A1016 O 113.8 95.0 61.3 120.9 58.4 170.0 REMARK 620 8 BTB A 701 O4 60.6 134.2 73.3 74.3 130.7 59.1 130.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 TB A 703 TB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1019 O REMARK 620 2 ASP A 471 OD2 125.7 REMARK 620 3 HOH A1018 O 61.7 64.9 REMARK 620 4 HOH A1020 O 142.8 91.3 151.6 REMARK 620 5 HOH A1002 O 90.9 82.9 73.2 89.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BTB A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TB A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TB A 703 DBREF 4ESQ A 435 626 UNP A5U1W4 A5U1W4_MYCTA 83332 83523 SEQADV 4ESQ GLY A 433 UNP A5U1W4 EXPRESSION TAG SEQADV 4ESQ HIS A 434 UNP A5U1W4 EXPRESSION TAG SEQRES 1 A 194 GLY HIS GLN PRO VAL ALA GLU GLU ARG LEU SER ALA LEU SEQRES 2 A 194 LEU LEU ASN SER SER GLU VAL ASN ALA VAL MET GLY SER SEQRES 3 A 194 SER SER MET GLN PRO GLY LYS PRO ILE THR SER MET ASP SEQRES 4 A 194 SER SER PRO VAL THR VAL SER LEU PRO ASP CYS GLN GLY SEQRES 5 A 194 ALA LEU TYR THR SER GLN ASP PRO VAL TYR ALA GLY THR SEQRES 6 A 194 GLY TYR THR ALA ILE ASN GLY LEU ILE SER SER GLU PRO SEQRES 7 A 194 GLY ASP ASN TYR GLU HIS TRP VAL ASN GLN ALA VAL VAL SEQRES 8 A 194 ALA PHE PRO THR ALA ASP LYS ALA ARG ALA PHE VAL GLN SEQRES 9 A 194 THR SER ALA ASP LYS TRP LYS ASN CYS ALA GLY LYS THR SEQRES 10 A 194 VAL THR VAL THR ASN LYS ALA LYS THR TYR ARG TRP THR SEQRES 11 A 194 PHE ALA ASP VAL LYS GLY SER PRO PRO THR ILE THR VAL SEQRES 12 A 194 ILE ASP THR GLN GLU GLY ALA GLU GLY TRP GLU CYS GLN SEQRES 13 A 194 ARG ALA MET SER VAL ALA ASN ASN VAL VAL VAL ASP VAL SEQRES 14 A 194 ASN ALA CYS GLY TYR GLN ILE THR ASN GLN ALA GLY GLN SEQRES 15 A 194 ILE ALA ALA LYS ILE VAL ASP LYS VAL ASN LYS GLU HET BTB A 701 14 HET TB A 702 1 HET TB A 703 1 HETNAM BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- HETNAM 2 BTB PROPANE-1,3-DIOL HETNAM TB TERBIUM(III) ION HETSYN BTB BIS-TRIS BUFFER FORMUL 2 BTB C8 H19 N O5 FORMUL 3 TB 2(TB 3+) FORMUL 5 HOH *221(H2 O) HELIX 1 1 ALA A 438 LEU A 446 5 9 HELIX 2 2 ASN A 448 GLY A 457 1 10 HELIX 3 3 LEU A 479 ASP A 481 5 3 HELIX 4 4 CYS A 482 TYR A 487 1 6 HELIX 5 5 GLN A 490 ALA A 495 1 6 HELIX 6 6 THR A 527 ASN A 544 1 18 HELIX 7 7 ASN A 610 LYS A 625 1 16 SHEET 1 A 9 GLN A 462 PRO A 463 0 SHEET 2 A 9 ALA A 501 SER A 508 -1 O SER A 508 N GLN A 462 SHEET 3 A 9 HIS A 516 ALA A 524 -1 O VAL A 518 N SER A 507 SHEET 4 A 9 VAL A 597 GLY A 605 -1 O CYS A 604 N TRP A 517 SHEET 5 A 9 GLU A 586 ALA A 594 -1 N GLN A 588 O ALA A 603 SHEET 6 A 9 ILE A 573 GLN A 579 -1 N VAL A 575 O ARG A 589 SHEET 7 A 9 LYS A 557 PHE A 563 -1 N THR A 562 O THR A 578 SHEET 8 A 9 THR A 549 ASN A 554 -1 N VAL A 552 O TYR A 559 SHEET 9 A 9 THR A 476 VAL A 477 -1 N THR A 476 O THR A 553 SSBOND 1 CYS A 482 CYS A 545 1555 1555 2.04 SSBOND 2 CYS A 587 CYS A 604 1555 1555 2.05 LINK O1 BTB A 701 TB TB A 702 1555 1555 2.34 LINK O8 BTB A 701 TB TB A 702 1555 1555 2.38 LINK TB TB A 702 O HOH A1017 1555 1555 2.42 LINK TB TB A 703 O HOH A1019 1555 1555 2.47 LINK OD2 ASP A 471 TB TB A 703 1555 1555 2.52 LINK O6 BTB A 701 TB TB A 702 1555 1555 2.56 LINK TB TB A 702 O HOH A1008 1555 1555 2.57 LINK TB TB A 703 O HOH A1018 1555 1555 2.60 LINK N BTB A 701 TB TB A 702 1555 1555 2.62 LINK TB TB A 702 O HOH A1016 1555 1555 2.70 LINK TB TB A 703 O HOH A1020 1555 1555 2.81 LINK O4 BTB A 701 TB TB A 702 1555 1555 3.07 LINK TB TB A 703 O HOH A1002 1555 1555 3.27 CISPEP 1 PRO A 570 PRO A 571 0 -0.44 SITE 1 AC1 12 ASP A 512 ASN A 513 TYR A 514 GLN A 579 SITE 2 AC1 12 GLU A 583 TRP A 585 TB A 702 HOH A 980 SITE 3 AC1 12 HOH A 987 HOH A1008 HOH A1014 HOH A1017 SITE 1 AC2 4 BTB A 701 HOH A1008 HOH A1016 HOH A1017 SITE 1 AC3 4 ASP A 471 HOH A1018 HOH A1019 HOH A1020 CRYST1 47.455 35.923 49.308 90.00 98.36 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 0.021073 0.000000 0.003096 0.00000 SCALE2 0.000000 0.027837 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020498 0.00000