HEADER TRANSFERASE 17-FEB-10 2KUD TITLE NMR STRUCTURE OF THE PASTA DOMAIN 1 AND 2 OF MYCOBACTERIUM TITLE 2 TUBERCULOSIS OF PKNB COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PKNB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PASTA DOMAINS 1 AND 2, RESIDUES 355-491; COMPND 5 SYNONYM: PKNB; COMPND 6 EC: 2.7.11.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: RV0014C; 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: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET21-TEV KEYWDS KINASE, EXTERNAL DOMAIN, SIGNALING, STPK, RESUSCITATION, KEYWDS 2 SERINE/THREONINE-PROTEIN KINASE, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR P.BARTHE,G.MUKAMOLOVA,C.ROUMESTAND,M.COHEN-GONSAUD REVDAT 4 14-JUN-23 2KUD 1 REMARK REVDAT 3 26-FEB-20 2KUD 1 REMARK SEQADV REVDAT 2 26-MAY-10 2KUD 1 JRNL REVDAT 1 14-APR-10 2KUD 0 JRNL AUTH P.BARTHE,G.V.MUKAMOLOVA,C.ROUMESTAND,M.COHEN-GONSAUD JRNL TITL THE STRUCTURE OF PKNB EXTRACELLULAR PASTA DOMAIN FROM JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS SUGGESTS A LIGAND-DEPENDENT JRNL TITL 3 KINASE ACTIVATION JRNL REF STRUCTURE V. 18 606 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20462494 JRNL DOI 10.1016/J.STR.2010.02.013 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE REMARK 3 -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: LIKE RECOORD DATABASE REMARK 4 REMARK 4 2KUD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000101583. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 4.6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6MM [U-100% 15N] PKNB_PASTA12; REMARK 210 20MM SODIUM ACETATE; 95% H2O/5% REMARK 210 D2O; 0.6MM [U-100% 13C; U-100% REMARK 210 15N] PKNB_PASTA12; 20MM SODIUM REMARK 210 ACETATE; 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-15N REMARK 210 TOCSY; 3D HNCA; 3D HN(COCA)CB; REMARK 210 3D HNCACB; 3D HNCO; 3D HNCACO REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS IN REMARK 210 A HYDRATED ENVIRONMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-30 REMARK 465 RES C SSSEQI REMARK 465 GLY A 352 REMARK 465 HIS A 353 REMARK 465 MET A 354 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 OD1 ASP A 364 HG1 THR A 402 1.58 REMARK 500 OE1 GLU A 439 HZ3 LYS A 443 1.59 REMARK 500 HG SER A 369 OD2 ASP A 372 1.60 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 1 THR A 393 74.52 -101.83 REMARK 500 2 ASP A 391 -176.04 -171.95 REMARK 500 2 ASP A 397 -9.05 -57.14 REMARK 500 3 THR A 393 36.91 -90.61 REMARK 500 3 PRO A 404 -14.46 -48.64 REMARK 500 4 THR A 393 35.45 -89.30 REMARK 500 5 VAL A 365 45.56 -89.82 REMARK 500 5 THR A 393 71.13 -101.57 REMARK 500 5 ASP A 397 -8.42 -56.81 REMARK 500 6 ASP A 391 174.75 170.06 REMARK 500 6 PRO A 404 -31.26 -33.73 REMARK 500 7 ASP A 391 -169.32 172.20 REMARK 500 7 ASP A 397 -7.26 -57.68 REMARK 500 8 ASP A 391 166.76 168.56 REMARK 500 8 ASP A 397 -8.21 -56.46 REMARK 500 8 ALA A 474 24.74 -71.17 REMARK 500 9 ASP A 397 -9.50 -57.74 REMARK 500 9 PRO A 404 -7.38 -56.65 REMARK 500 10 ARG A 358 38.07 -96.80 REMARK 500 10 ASP A 391 -175.00 -179.62 REMARK 500 10 ASP A 397 -8.12 -57.03 REMARK 500 11 VAL A 365 35.73 -81.64 REMARK 500 11 ASP A 391 -176.64 -171.09 REMARK 500 11 THR A 393 73.47 -101.86 REMARK 500 12 ASP A 391 -175.12 -173.14 REMARK 500 13 PRO A 363 135.79 -37.99 REMARK 500 13 ASP A 391 -166.85 175.18 REMARK 500 13 ASP A 397 -8.52 -59.67 REMARK 500 13 THR A 436 161.85 178.45 REMARK 500 15 ASP A 391 -168.37 177.13 REMARK 500 15 SER A 392 -1.29 -143.25 REMARK 500 15 ASP A 397 -7.93 -55.87 REMARK 500 15 VAL A 432 -7.52 -146.25 REMARK 500 16 ASP A 391 -166.48 179.75 REMARK 500 16 ASP A 397 -8.79 -57.14 REMARK 500 16 PRO A 404 -36.03 -37.04 REMARK 500 17 ASP A 391 -170.36 174.95 REMARK 500 17 THR A 393 58.82 -91.72 REMARK 500 17 ASP A 397 -8.37 -57.64 REMARK 500 17 ASP A 414 -166.79 -114.31 REMARK 500 18 ASP A 391 -164.71 174.06 REMARK 500 18 SER A 392 -0.53 -142.34 REMARK 500 18 ASP A 397 -8.56 -56.28 REMARK 500 19 ASP A 391 -167.61 163.55 REMARK 500 19 ASP A 397 -9.93 -57.03 REMARK 500 19 ALA A 474 19.19 -68.92 REMARK 500 21 ASP A 391 -165.18 164.85 REMARK 500 21 ASP A 397 -9.90 -55.25 REMARK 500 21 PRO A 404 -30.70 -37.23 REMARK 500 22 GLN A 368 -168.12 -122.57 REMARK 500 REMARK 500 THIS ENTRY HAS 74 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 9 ARG A 366 0.10 SIDE CHAIN REMARK 500 18 ARG A 380 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KUE RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PASTA DOMAIN 2 AND 3 REMARK 900 RELATED ID: 2KUF RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PASTA DOMAIN 3 AND 4 REMARK 900 RELATED ID: 2KUI RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PASTA DOMAIN REMARK 900 RELATED ID: 16732 RELATED DB: BMRB DBREF 2KUD A 355 491 UNP P0A5S4 PKNB_MYCTU 355 491 SEQADV 2KUD GLY A 352 UNP P0A5S4 EXPRESSION TAG SEQADV 2KUD HIS A 353 UNP P0A5S4 EXPRESSION TAG SEQADV 2KUD MET A 354 UNP P0A5S4 EXPRESSION TAG SEQRES 1 A 140 GLY HIS MET GLY ILE THR ARG ASP VAL GLN VAL PRO ASP SEQRES 2 A 140 VAL ARG GLY GLN SER SER ALA ASP ALA ILE ALA THR LEU SEQRES 3 A 140 GLN ASN ARG GLY PHE LYS ILE ARG THR LEU GLN LYS PRO SEQRES 4 A 140 ASP SER THR ILE PRO PRO ASP HIS VAL ILE GLY THR ASP SEQRES 5 A 140 PRO ALA ALA ASN THR SER VAL SER ALA GLY ASP GLU ILE SEQRES 6 A 140 THR VAL ASN VAL SER THR GLY PRO GLU GLN ARG GLU ILE SEQRES 7 A 140 PRO ASP VAL SER THR LEU THR TYR ALA GLU ALA VAL LYS SEQRES 8 A 140 LYS LEU THR ALA ALA GLY PHE GLY ARG PHE LYS GLN ALA SEQRES 9 A 140 ASN SER PRO SER THR PRO GLU LEU VAL GLY LYS VAL ILE SEQRES 10 A 140 GLY THR ASN PRO PRO ALA ASN GLN THR SER ALA ILE THR SEQRES 11 A 140 ASN VAL VAL ILE ILE ILE VAL GLY SER GLY HELIX 1 1 SER A 369 GLY A 381 1 13 HELIX 2 2 ASP A 403 THR A 408 1 6 HELIX 3 3 VAL A 432 LEU A 435 5 4 HELIX 4 4 THR A 436 ALA A 447 1 12 HELIX 5 5 THR A 460 VAL A 464 5 5 SHEET 1 A 2 ASP A 359 VAL A 360 0 SHEET 2 A 2 VAL A 410 SER A 411 -1 O VAL A 410 N VAL A 360 SHEET 1 B 2 LYS A 383 ASP A 391 0 SHEET 2 B 2 GLU A 415 PRO A 424 1 O VAL A 418 N ARG A 385 SHEET 1 C 2 GLN A 426 GLU A 428 0 SHEET 2 C 2 THR A 477 ALA A 479 -1 O SER A 478 N ARG A 427 SHEET 1 D 3 PHE A 452 SER A 457 0 SHEET 2 D 3 VAL A 484 GLY A 489 1 O ILE A 486 N ALA A 455 SHEET 3 D 3 VAL A 467 THR A 470 -1 N ILE A 468 O ILE A 487 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1