PDB Short entry for 2JW6 HEADER TRANSCRIPTION 08-OCT-07 2JW6 TITLE SOLUTION STRUCTURE OF THE DEAF1 MYND DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEFORMED EPIDERMAL AUTOREGULATORY FACTOR 1 HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MYND DOMAIN; COMPND 5 SYNONYM: NUCLEAR DEAF-1- RELATED TRANSCRIPTIONAL REGULATOR, NUDR, COMPND 6 SUPPRESSIN, ZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 5; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET24D KEYWDS ZINC BINDING DOMAIN, TRANSCRIPTION, DISEASE MUTATION, DNA-BINDING, KEYWDS 2 METAL-BINDING, NUCLEUS, PHOSPHORYLATION, SECRETED, TRANSCRIPTION KEYWDS 3 REGULATION, ZINC-FINGER EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.SPADACCINI,H.PERRIN,M.BOTTOMLEY,S.ANSIEU,M.SATTLER REVDAT 4 10-APR-13 2JW6 1 JRNL REMARK VERSN REVDAT 3 26-MAY-10 2JW6 1 REMARK REVDAT 2 24-FEB-09 2JW6 1 VERSN REVDAT 1 25-DEC-07 2JW6 0 SPRSDE 25-DEC-07 2JW6 2FV6 JRNL AUTH R.SPADACCINI,H.PERRIN,M.J.BOTTOMLEY,S.ANSIEAU,M.SATTLER JRNL TITL RETRACTION NOTICE TO "STRUCTURE AND FUNCTIONAL ANALYSIS OF JRNL TITL 2 THE MYND DOMAIN" [J. MOL. BIOL. (2006) 358, 498-508]. JRNL REF J.MOL.BIOL. V. 376 1523 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18286714 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.SPADACCINI,H.PERRIN,M.J.BOTTOMLEY,S.ANSIEAU,M.SATTLER REMARK 1 TITL STRUCTURE AND FUNCTIONAL ANALYSIS OF THE MYND DOMAIN. REMARK 1 REF J.MOL.BIOL. V. 358 498 2006 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 16527309 REMARK 1 DOI 10.1016/J.JMB.2006.01.087 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MOLECULAR DYNAMICS THE NMR ENSEMBLE HAS REMARK 3 BEEN REFINED IN A SHELL OF WATER MOLECULES. REFINEMENT DETAILS REMARK 3 CAN BE FOUND IN THE JRNL CITATION ABOVE AND LINGE ET AL. REMARK 3 STRUCTURES WERE CALCULATED WITH ARIA 1.2 IN COMBINATION WITH CNS. REMARK 4 REMARK 4 2JW6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-OCT-07. REMARK 100 THE RCSB ID CODE IS RCSB100366. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 20MM PHOSPHATE, 100MM NACL REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 0,4 MM [U-100% 13C; U-100% 15N] REMARK 210 MYND, 4 MM DTT, 20 MM SODIUM REMARK 210 PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY; 3D HNCA; 3D 1H- REMARK 210 15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, ARIA REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A 493 REMARK 465 ALA A 494 REMARK 465 MET A 495 REMARK 465 ASP A 496 REMARK 465 ALA A 497 REMARK 465 GLU A 498 REMARK 465 ARG A 499 REMARK 465 LYS A 500 REMARK 465 GLU A 501 REMARK 465 GLN A 502 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 506 -40.91 -139.00 REMARK 500 1 CYS A 507 -87.45 -137.26 REMARK 500 1 ARG A 509 -178.83 -65.07 REMARK 500 1 ALA A 511 156.82 164.87 REMARK 500 1 MET A 512 -62.96 -100.14 REMARK 500 1 CYS A 515 109.24 -38.75 REMARK 500 1 THR A 516 34.56 -73.84 REMARK 500 1 CYS A 518 -38.19 -164.39 REMARK 500 2 ASN A 506 -43.33 -138.28 REMARK 500 2 CYS A 507 -89.06 -148.10 REMARK 500 2 ARG A 509 -162.89 -75.43 REMARK 500 2 ALA A 511 153.56 170.77 REMARK 500 2 MET A 512 -72.20 -110.99 REMARK 500 2 THR A 516 22.46 -71.50 REMARK 500 2 CYS A 518 -39.41 -158.99 REMARK 500 3 VAL A 505 7.74 -69.85 REMARK 500 3 CYS A 507 -48.44 -149.44 REMARK 500 3 ALA A 511 135.06 71.19 REMARK 500 3 CYS A 515 114.18 -39.05 REMARK 500 3 CYS A 518 -38.55 -164.62 REMARK 500 3 TRP A 533 6.25 -65.80 REMARK 500 4 VAL A 505 21.44 -75.25 REMARK 500 4 ASN A 506 -32.26 -145.86 REMARK 500 4 CYS A 507 -93.36 -140.84 REMARK 500 4 ARG A 509 138.92 65.76 REMARK 500 4 ALA A 511 148.03 76.51 REMARK 500 4 CYS A 515 107.08 -43.50 REMARK 500 4 CYS A 518 -42.74 -153.46 REMARK 500 5 VAL A 505 20.58 -74.27 REMARK 500 5 ASN A 506 -38.78 -143.01 REMARK 500 5 CYS A 507 -79.44 -136.03 REMARK 500 5 ALA A 511 155.01 73.36 REMARK 500 5 MET A 512 -63.41 -92.44 REMARK 500 5 CYS A 515 107.83 -40.32 REMARK 500 5 CYS A 518 -41.14 -160.87 REMARK 500 5 HIS A 519 31.35 71.43 REMARK 500 5 TRP A 533 4.96 -67.16 REMARK 500 6 ASN A 506 -31.45 -142.45 REMARK 500 6 CYS A 507 -99.77 -139.26 REMARK 500 6 ARG A 509 151.65 -36.38 REMARK 500 6 GLU A 510 21.37 -68.71 REMARK 500 6 ALA A 511 120.65 70.41 REMARK 500 6 CYS A 515 106.77 -38.84 REMARK 500 6 CYS A 518 -48.32 -158.44 REMARK 500 6 HIS A 519 33.82 72.10 REMARK 500 7 CYS A 507 -82.36 -133.48 REMARK 500 7 ARG A 509 142.67 -35.55 REMARK 500 7 GLU A 510 20.13 -68.84 REMARK 500 7 ALA A 511 137.64 73.85 REMARK 500 7 THR A 516 0.13 -64.12 REMARK 500 REMARK 500 THIS ENTRY HAS 72 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 TYR A 523 0.07 SIDE CHAIN 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 1 ZN A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 536 NE2 REMARK 620 2 CYS A 515 SG 111.1 REMARK 620 3 CYS A 540 SG 108.0 108.8 REMARK 620 4 CYS A 518 SG 108.7 108.9 111.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 528 SG REMARK 620 2 CYS A 507 SG 108.2 REMARK 620 3 CYS A 524 SG 109.5 108.7 REMARK 620 4 CYS A 504 SG 108.9 109.0 112.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 602 DBREF 2JW6 A 496 544 UNP O75398 DEAF1_HUMAN 496 544 SEQADV 2JW6 GLY A 493 UNP O75398 EXPRESSION TAG SEQADV 2JW6 ALA A 494 UNP O75398 EXPRESSION TAG SEQADV 2JW6 MET A 495 UNP O75398 EXPRESSION TAG SEQRES 1 A 52 GLY ALA MET ASP ALA GLU ARG LYS GLU GLN SER CYS VAL SEQRES 2 A 52 ASN CYS GLY ARG GLU ALA MET SER GLU CYS THR GLY CYS SEQRES 3 A 52 HIS LYS VAL ASN TYR CYS SER THR PHE CYS GLN ARG LYS SEQRES 4 A 52 ASP TRP LYS ASP HIS GLN HIS ILE CYS GLY GLN SER ALA HET ZN A 601 1 HET ZN A 602 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 SER A 525 TRP A 533 1 9 HELIX 2 2 LYS A 534 ILE A 539 5 6 SHEET 1 A 2 SER A 513 GLU A 514 0 SHEET 2 A 2 ASN A 522 TYR A 523 -1 O TYR A 523 N SER A 513 LINK NE2 HIS A 536 ZN ZN A 602 1555 1555 1.99 LINK SG CYS A 528 ZN ZN A 601 1555 1555 2.27 LINK SG CYS A 507 ZN ZN A 601 1555 1555 2.27 LINK SG CYS A 524 ZN ZN A 601 1555 1555 2.29 LINK SG CYS A 504 ZN ZN A 601 1555 1555 2.29 LINK SG CYS A 515 ZN ZN A 602 1555 1555 2.30 LINK SG CYS A 540 ZN ZN A 602 1555 1555 2.30 LINK SG CYS A 518 ZN ZN A 602 1555 1555 2.30 SITE 1 AC1 4 CYS A 504 CYS A 507 CYS A 524 CYS A 528 SITE 1 AC2 4 CYS A 515 CYS A 518 HIS A 536 CYS A 540 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