HEADER TRANSFERASE 17-FEB-10 2KUI TITLE NMR STRUCTURE OF THE PASTA DOMAIN OF MYCOBACTERIUM TUBERCULOSIS OF TITLE 2 PKNB COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PKNB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PASTA DOMAINS 1,2,3 AND 4, RESIDUES 355-626; 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 28 AUTHOR P.BARTHE,G.MUKAMOLOVA,C.ROUMESTAND,M.COHEN-GONSAUD REVDAT 3 16-MAR-22 2KUI 1 REMARK SEQADV REVDAT 2 26-MAY-10 2KUI 1 JRNL REVDAT 1 14-APR-10 2KUI 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 3 THIS ENTRY IS BUILT FROM 3 PKNB PASTA MODULES (ENTRIES 2KUD, 2KUE REMARK 3 AND 2KUF). REMARK 4 REMARK 4 2KUI 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_1000101588. 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] REMARK 210 PKNB_PASTA1234; 20MM SODIUM REMARK 210 ACETATE; 95% H2O/5% D2O; 0.6MM REMARK 210 [U-100% 13C; U-100% 15N] PKNB_ REMARK 210 PASTA1234; 20MM SODIUM ACETATE; REMARK 210 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 : 28 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 1-28 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 HG1 THR A 460 OE1 GLU A 462 1.56 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 GLN A 368 -89.35 -111.10 REMARK 500 1 ASP A 391 148.04 87.03 REMARK 500 1 PRO A 395 114.84 -23.33 REMARK 500 1 PRO A 404 3.09 -64.34 REMARK 500 1 THR A 436 66.40 -108.61 REMARK 500 1 ASN A 601 5.32 58.37 REMARK 500 2 VAL A 365 36.97 -82.93 REMARK 500 2 GLN A 368 -153.20 -110.87 REMARK 500 2 ASP A 391 158.46 174.99 REMARK 500 2 PRO A 395 129.92 -39.97 REMARK 500 2 ASP A 397 -8.47 -59.78 REMARK 500 2 PRO A 404 -4.65 -56.31 REMARK 500 2 THR A 436 40.95 -106.61 REMARK 500 2 PHE A 517 98.89 -68.70 REMARK 500 2 ASN A 601 12.80 46.34 REMARK 500 3 GLN A 368 -85.08 -106.48 REMARK 500 3 ASP A 391 178.59 86.41 REMARK 500 3 PRO A 395 116.94 -28.97 REMARK 500 3 ASP A 397 -9.24 -57.63 REMARK 500 3 THR A 436 49.96 -102.65 REMARK 500 3 ASN A 559 -8.74 72.53 REMARK 500 3 HIS A 600 -148.92 -150.49 REMARK 500 4 GLN A 368 -82.06 -107.82 REMARK 500 4 ASP A 391 159.25 158.43 REMARK 500 4 ASP A 397 -9.88 -56.38 REMARK 500 4 PRO A 404 -3.09 -52.80 REMARK 500 4 THR A 436 65.15 -109.42 REMARK 500 4 GLN A 476 -165.49 -119.81 REMARK 500 4 ALA A 595 -9.56 -156.33 REMARK 500 4 HIS A 600 37.29 -145.09 REMARK 500 4 ASN A 601 90.37 -68.70 REMARK 500 5 ARG A 358 -33.29 -134.95 REMARK 500 5 GLN A 368 -154.00 -110.58 REMARK 500 5 ASP A 391 162.47 176.85 REMARK 500 5 ASP A 397 -8.69 -57.21 REMARK 500 5 THR A 436 57.41 -105.95 REMARK 500 5 ALA A 493 37.50 -147.43 REMARK 500 5 VAL A 500 89.07 -162.54 REMARK 500 5 ASN A 601 -2.11 57.48 REMARK 500 5 ASN A 615 172.57 -54.99 REMARK 500 6 ARG A 358 72.44 -100.38 REMARK 500 6 GLN A 368 -81.86 -104.08 REMARK 500 6 ASP A 391 160.49 173.71 REMARK 500 6 PRO A 395 -173.60 -66.14 REMARK 500 6 ASP A 397 -9.81 -57.88 REMARK 500 6 THR A 436 41.40 -92.54 REMARK 500 6 HIS A 600 102.83 56.10 REMARK 500 6 ASN A 615 144.23 -39.53 REMARK 500 7 VAL A 365 30.35 -92.46 REMARK 500 7 GLN A 368 -155.84 -112.19 REMARK 500 REMARK 500 THIS ENTRY HAS 230 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 1 ARG A 616 0.10 SIDE CHAIN REMARK 500 5 ARG A 623 0.07 SIDE CHAIN REMARK 500 6 ARG A 616 0.10 SIDE CHAIN REMARK 500 10 ARG A 602 0.08 SIDE CHAIN REMARK 500 12 ARG A 366 0.11 SIDE CHAIN REMARK 500 18 ARG A 427 0.08 SIDE CHAIN REMARK 500 22 ARG A 366 0.10 SIDE CHAIN REMARK 500 26 ARG A 577 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KUD RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PASTA DOMAIN 1 AND 2 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 DBREF 2KUI A 355 626 UNP P0A5S4 PKNB_MYCTU 355 626 SEQADV 2KUI GLY A 352 UNP P0A5S4 EXPRESSION TAG SEQADV 2KUI HIS A 353 UNP P0A5S4 EXPRESSION TAG SEQADV 2KUI MET A 354 UNP P0A5S4 EXPRESSION TAG SEQRES 1 A 275 GLY HIS MET GLY ILE THR ARG ASP VAL GLN VAL PRO ASP SEQRES 2 A 275 VAL ARG GLY GLN SER SER ALA ASP ALA ILE ALA THR LEU SEQRES 3 A 275 GLN ASN ARG GLY PHE LYS ILE ARG THR LEU GLN LYS PRO SEQRES 4 A 275 ASP SER THR ILE PRO PRO ASP HIS VAL ILE GLY THR ASP SEQRES 5 A 275 PRO ALA ALA ASN THR SER VAL SER ALA GLY ASP GLU ILE SEQRES 6 A 275 THR VAL ASN VAL SER THR GLY PRO GLU GLN ARG GLU ILE SEQRES 7 A 275 PRO ASP VAL SER THR LEU THR TYR ALA GLU ALA VAL LYS SEQRES 8 A 275 LYS LEU THR ALA ALA GLY PHE GLY ARG PHE LYS GLN ALA SEQRES 9 A 275 ASN SER PRO SER THR PRO GLU LEU VAL GLY LYS VAL ILE SEQRES 10 A 275 GLY THR ASN PRO PRO ALA ASN GLN THR SER ALA ILE THR SEQRES 11 A 275 ASN VAL VAL ILE ILE ILE VAL GLY SER GLY PRO ALA THR SEQRES 12 A 275 LYS ASP ILE PRO ASP VAL ALA GLY GLN THR VAL ASP VAL SEQRES 13 A 275 ALA GLN LYS ASN LEU ASN VAL TYR GLY PHE THR LYS PHE SEQRES 14 A 275 SER GLN ALA SER VAL ASP SER PRO ARG PRO ALA GLY GLU SEQRES 15 A 275 VAL THR GLY THR ASN PRO PRO ALA GLY THR THR VAL PRO SEQRES 16 A 275 VAL ASP SER VAL ILE GLU LEU GLN VAL SER LYS GLY ASN SEQRES 17 A 275 GLN PHE VAL MET PRO ASP LEU SER GLY MET PHE TRP VAL SEQRES 18 A 275 ASP ALA GLU PRO ARG LEU ARG ALA LEU GLY TRP THR GLY SEQRES 19 A 275 MET LEU ASP LYS GLY ALA ASP VAL ASP ALA GLY GLY SER SEQRES 20 A 275 GLN HIS ASN ARG VAL VAL TYR GLN ASN PRO PRO ALA GLY SEQRES 21 A 275 THR GLY VAL ASN ARG ASP GLY ILE ILE THR LEU ARG PHE SEQRES 22 A 275 GLY GLN HELIX 1 1 SER A 369 GLY A 381 1 13 HELIX 2 2 THR A 436 ALA A 447 1 12 HELIX 3 3 THR A 504 TYR A 515 1 12 HELIX 4 4 PHE A 570 LEU A 581 1 12 HELIX 5 5 GLY A 596 HIS A 600 5 5 SHEET 1 A 2 VAL A 360 GLN A 361 0 SHEET 2 A 2 SER A 409 VAL A 410 -1 O VAL A 410 N VAL A 360 SHEET 1 B 2 LYS A 383 PRO A 390 0 SHEET 2 B 2 GLU A 415 THR A 422 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 LYS A 453 SHEET 3 D 3 VAL A 467 THR A 470 -1 N ILE A 468 O ILE A 487 SHEET 1 E 2 THR A 494 ASP A 496 0 SHEET 2 E 2 THR A 544 PRO A 546 -1 O VAL A 545 N LYS A 495 SHEET 1 F 3 LYS A 519 ASP A 526 0 SHEET 2 F 3 VAL A 550 LYS A 557 1 O LEU A 553 N SER A 521 SHEET 3 F 3 VAL A 534 THR A 537 -1 N GLY A 536 O GLN A 554 SHEET 1 G 2 GLN A 560 VAL A 562 0 SHEET 2 G 2 GLY A 613 ASN A 615 -1 O VAL A 614 N PHE A 561 SHEET 1 H 2 LEU A 587 ASP A 588 0 SHEET 2 H 2 ILE A 620 THR A 621 1 O ILE A 620 N ASP A 588 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