HEADER CHAPERONE 23-NOV-99 1DG4 TITLE NMR STRUCTURE OF THE SUBSTRATE BINDING DOMAIN OF DNAK IN THE APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNAK; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SUBSTRATE BINDING DOMAIN; COMPND 5 OTHER_DETAILS: MOLECULAR CHAPERONE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS DNAK, CHAPERONE, SUBSTRATE BINDING DOMAIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.PELLECCHIA,D.L.MONTGOMERY,S.Y.STEVENS,C.W.VAN DER KOOI,H.FENG, AUTHOR 2 L.M.GIERASCH,E.R.P.ZUIDERWEG REVDAT 6 22-MAY-24 1DG4 1 REMARK REVDAT 5 16-FEB-22 1DG4 1 REMARK REVDAT 4 24-FEB-09 1DG4 1 VERSN REVDAT 3 01-APR-03 1DG4 1 JRNL REVDAT 2 01-APR-00 1DG4 1 JRNL REMARK REVDAT 1 08-DEC-99 1DG4 0 JRNL AUTH M.PELLECCHIA,D.L.MONTGOMERY,S.Y.STEVENS,C.W.VANDER KOOI, JRNL AUTH 2 H.P.FENG,L.M.GIERASCH,E.R.ZUIDERWEG JRNL TITL STRUCTURAL INSIGHTS INTO SUBSTRATE BINDING BY THE MOLECULAR JRNL TITL 2 CHAPERONE DNAK. JRNL REF NAT.STRUCT.BIOL. V. 7 298 2000 JRNL REFN ISSN 1072-8368 JRNL PMID 10742174 JRNL DOI 10.1038/74062 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 2.6, FANTOM 1.0 REMARK 3 AUTHORS : VARIAN (VNMR), BRAUN (FANTOM) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DG4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000010056. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 303; 303; 303 REMARK 210 PH : 6.8; 6.8; 6.8; 6.8 REMARK 210 IONIC STRENGTH : 10MM NA PHOSPHATE; 10MM NA REMARK 210 PHOSPHATE; 10MM NA PHOSPHATE; REMARK 210 10MM NA PHOSPHATE REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM U15N; 10MM PHOSPHATE BUFFER REMARK 210 NA; 1MM U15N,13C; 10MM PHOSPHATE REMARK 210 BUFFER NA; 1MM U15N,13C; 10MM REMARK 210 PHOSPHATE BUFFER NA; 1MM 10% 13C; REMARK 210 10MM PHOSPHATE BUFFER NA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_HNCA, 3D_ REMARK 210 HN(CA)HA; H(C)CH_TOCSY, (H)CCH_ REMARK 210 TOCSY; 13C,1H_HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PROSA 3.7, DYANA 1.5, XEASY 2.6 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,TARGET REMARK 210 FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 ASP A 393 REMARK 465 VAL A 394 REMARK 465 THR A 395 REMARK 465 PRO A 396 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 ASN A 415 50.97 -111.35 REMARK 500 1 VAL A 425 55.21 32.57 REMARK 500 1 ARG A 445 136.74 -171.53 REMARK 500 1 LEU A 454 13.79 -148.20 REMARK 500 1 SER A 505 81.81 51.47 REMARK 500 2 SER A 398 93.36 -60.84 REMARK 500 2 THR A 410 73.99 -65.35 REMARK 500 2 THR A 416 60.85 -113.80 REMARK 500 2 THR A 417 -75.91 67.18 REMARK 500 2 ILE A 418 92.95 60.78 REMARK 500 2 SER A 423 51.89 -149.52 REMARK 500 2 GLU A 444 39.38 -145.32 REMARK 500 2 LEU A 454 53.41 -152.10 REMARK 500 2 ARG A 467 -44.48 83.01 REMARK 500 2 SER A 504 -179.43 63.54 REMARK 500 3 THR A 410 82.73 -65.41 REMARK 500 3 ASN A 415 63.44 62.47 REMARK 500 3 THR A 416 63.48 -69.87 REMARK 500 3 PHE A 426 39.52 -163.41 REMARK 500 3 GLU A 444 38.21 -158.77 REMARK 500 3 LYS A 446 -76.39 68.44 REMARK 500 3 LEU A 454 21.17 -151.54 REMARK 500 3 ASN A 463 80.34 -152.44 REMARK 500 3 SER A 504 115.95 74.05 REMARK 500 3 SER A 505 -166.96 60.26 REMARK 500 4 ASN A 415 61.49 -111.42 REMARK 500 4 THR A 416 46.66 -92.62 REMARK 500 4 THR A 417 -77.38 61.31 REMARK 500 4 ILE A 418 132.86 67.18 REMARK 500 4 GLN A 424 174.83 65.01 REMARK 500 4 SER A 434 -51.15 -160.19 REMARK 500 4 GLU A 444 41.08 -161.02 REMARK 500 4 LEU A 454 48.61 -150.21 REMARK 500 4 SER A 504 142.13 -171.39 REMARK 500 4 SER A 505 -58.34 -162.35 REMARK 500 5 THR A 410 73.48 -67.73 REMARK 500 5 THR A 417 -76.80 52.64 REMARK 500 5 ILE A 418 130.08 67.09 REMARK 500 5 SER A 423 -89.46 -145.15 REMARK 500 5 VAL A 425 170.58 62.92 REMARK 500 5 ARG A 445 42.36 -101.56 REMARK 500 5 LYS A 446 -89.28 63.40 REMARK 500 5 LEU A 454 46.30 -146.59 REMARK 500 5 ALA A 465 78.21 -163.40 REMARK 500 5 ARG A 467 95.33 -69.53 REMARK 500 5 GLN A 471 152.41 75.44 REMARK 500 5 ALA A 503 51.45 -103.22 REMARK 500 5 SER A 504 -50.98 -165.23 REMARK 500 6 THR A 410 71.90 -66.88 REMARK 500 6 ASN A 415 61.62 62.78 REMARK 500 REMARK 500 THIS ENTRY HAS 218 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 411 ILE A 412 7 147.16 REMARK 500 ILE A 418 PRO A 419 7 -39.94 REMARK 500 LEU A 441 GLN A 442 7 149.39 REMARK 500 GLU A 473 VAL A 474 7 133.41 REMARK 500 ILE A 438 HIS A 439 8 149.86 REMARK 500 THR A 417 ILE A 418 9 144.07 REMARK 500 ILE A 438 HIS A 439 9 143.82 REMARK 500 GLN A 471 ILE A 472 9 148.74 REMARK 500 ILE A 418 PRO A 419 10 -73.40 REMARK 500 GLN A 424 VAL A 425 10 -141.09 REMARK 500 ALA A 465 PRO A 466 10 -147.99 REMARK 500 LYS A 495 GLU A 496 10 149.54 REMARK 500 ILE A 418 PRO A 419 12 -31.58 REMARK 500 MET A 469 PRO A 470 12 148.67 REMARK 500 ILE A 418 PRO A 419 14 -50.24 REMARK 500 ILE A 438 HIS A 439 14 135.37 REMARK 500 THR A 416 THR A 417 15 143.11 REMARK 500 ILE A 472 GLU A 473 15 149.93 REMARK 500 ILE A 418 PRO A 419 16 -34.88 REMARK 500 PRO A 419 THR A 420 16 -147.39 REMARK 500 THR A 417 ILE A 418 18 -140.56 REMARK 500 ILE A 438 HIS A 439 19 140.55 REMARK 500 PHE A 476 ASP A 477 19 -148.24 REMARK 500 THR A 403 MET A 404 20 -144.61 REMARK 500 MET A 404 GLY A 405 20 -148.83 REMARK 500 THR A 416 THR A 417 20 148.53 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 445 0.12 SIDE CHAIN REMARK 500 1 ARG A 467 0.09 SIDE CHAIN REMARK 500 3 ARG A 447 0.12 SIDE CHAIN REMARK 500 4 ARG A 445 0.11 SIDE CHAIN REMARK 500 5 ARG A 445 0.09 SIDE CHAIN REMARK 500 6 ARG A 447 0.08 SIDE CHAIN REMARK 500 7 ARG A 445 0.12 SIDE CHAIN REMARK 500 7 ARG A 447 0.08 SIDE CHAIN REMARK 500 8 ARG A 445 0.13 SIDE CHAIN REMARK 500 11 ARG A 445 0.09 SIDE CHAIN REMARK 500 15 ARG A 445 0.11 SIDE CHAIN REMARK 500 18 ARG A 445 0.09 SIDE CHAIN REMARK 500 19 ARG A 445 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DKZ RELATED DB: PDB REMARK 900 1DKZ CONTAINS THE SAME PROTEIN COMPLEXED WITH THE PEPTIDE NRLLLTG REMARK 900 RELATED ID: 2BPR RELATED DB: PDB REMARK 900 2BPR CONTAINS THE SAME PROTEIN INTRAMOLECULARLY BOUND WITH ITS N- REMARK 900 TERMINAL TAIL DBREF 1DG4 A 393 507 UNP P0A6Y8 DNAK_ECOLI 393 507 SEQRES 1 A 115 ASP VAL THR PRO LEU SER LEU GLY ILE GLU THR MET GLY SEQRES 2 A 115 GLY VAL MET THR THR LEU ILE ALA LYS ASN THR THR ILE SEQRES 3 A 115 PRO THR LYS HIS SER GLN VAL PHE SER THR ALA GLU ASP SEQRES 4 A 115 ASN GLN SER ALA VAL THR ILE HIS VAL LEU GLN GLY GLU SEQRES 5 A 115 ARG LYS ARG ALA ALA ASP ASN LYS SER LEU GLY GLN PHE SEQRES 6 A 115 ASN LEU ASP GLY ILE ASN PRO ALA PRO ARG GLY MET PRO SEQRES 7 A 115 GLN ILE GLU VAL THR PHE ASP ILE ASP ALA ASP GLY ILE SEQRES 8 A 115 LEU HIS VAL SER ALA LYS ASP LYS ASN SER GLY LYS GLU SEQRES 9 A 115 GLN LYS ILE THR ILE LYS ALA SER SER GLY LEU SHEET 1 A 4 VAL A 407 THR A 409 0 SHEET 2 A 4 LEU A 399 THR A 403 -1 O ILE A 401 N THR A 409 SHEET 3 A 4 ALA A 435 GLN A 442 -1 O HIS A 439 N GLU A 402 SHEET 4 A 4 LYS A 452 ASP A 460 -1 O LYS A 452 N GLN A 442 SHEET 1 B 4 THR A 420 HIS A 422 0 SHEET 2 B 4 ILE A 472 ILE A 478 -1 N PHE A 476 O HIS A 422 SHEET 3 B 4 LEU A 484 ASP A 490 -1 N HIS A 485 O ASP A 477 SHEET 4 B 4 GLU A 496 ILE A 501 -1 O GLN A 497 N ALA A 488 CISPEP 1 ILE A 418 PRO A 419 1 -21.42 CISPEP 2 ILE A 418 PRO A 419 2 20.01 CISPEP 3 ILE A 418 PRO A 419 3 -23.91 CISPEP 4 ILE A 418 PRO A 419 4 -1.59 CISPEP 5 ILE A 418 PRO A 419 5 0.43 CISPEP 6 ILE A 418 PRO A 419 6 -17.20 CISPEP 7 ILE A 418 PRO A 419 8 -15.80 CISPEP 8 ILE A 418 PRO A 419 9 16.70 CISPEP 9 ILE A 418 PRO A 419 11 -26.21 CISPEP 10 ILE A 418 PRO A 419 13 15.10 CISPEP 11 ILE A 418 PRO A 419 15 -2.95 CISPEP 12 ILE A 418 PRO A 419 17 18.87 CISPEP 13 ILE A 418 PRO A 419 18 -20.69 CISPEP 14 ILE A 418 PRO A 419 19 -13.38 CISPEP 15 ILE A 418 PRO A 419 20 -13.90 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