HEADER APOPTOSIS 19-JAN-13 2M3H TITLE STRUCTURE OF DIDO PHD DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEATH-INDUCER OBLITERATOR 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIO-1, HDIDO1, DEATH-ASSOCIATED TRANSCRIPTION FACTOR 1, COMPND 5 DATF-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DIDO1, C20ORF158, DATF1, KIAA0333; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET28 KEYWDS PHD DOMAIN, APOPTOSIS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.M.SANTIVERI,J.M.PEREZ-CANADILLAS,M.JIMENEZ REVDAT 2 14-JUN-23 2M3H 1 REMARK SEQADV LINK REVDAT 1 07-AUG-13 2M3H 0 JRNL AUTH C.M.SANTIVERI,M.F.GARCIA-MAYORAL,J.M.PEREZ-CANADILLAS, JRNL AUTH 2 M.A.JIMENEZ JRNL TITL NMR STRUCTURE NOTE: PHD DOMAIN FROM DEATH INDUCER JRNL TITL 2 OBLITERATOR PROTEIN AND ITS INTERACTION WITH H3K4ME3. JRNL REF J.BIOMOL.NMR V. 56 183 2013 JRNL REFN ISSN 0925-2738 JRNL PMID 23579637 JRNL DOI 10.1007/S10858-013-9726-X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, CYANA REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M3H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000103161. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6 MM DIDO PHD, 10 UM POTASSIUM REMARK 210 PHOSPHATE, 100 UM TCEP, 90% H2O, REMARK 210 10% D2O, 10 UM DSS, 90% H2O/10% REMARK 210 D2O; 0.4 MM [U-99% 13C; U-99% REMARK 210 15N] DIDO PHD, 10 UM POTASSIUM REMARK 210 PHOSPHATE, 100 UM TCEP, 0.01% REMARK 210 SODIUM AZIDE, 90% H2O, 10% D2O, REMARK 210 10 UM DSS, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H NOESY; 2D 1H-15N HSQC; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 3D REMARK 210 HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 HNHA; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, TALOS, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 6 46.83 -106.51 REMARK 500 1 TYR A 9 -57.42 -145.88 REMARK 500 1 CYS A 10 157.03 -47.75 REMARK 500 1 ARG A 13 69.95 62.55 REMARK 500 1 ASN A 17 43.05 -89.18 REMARK 500 1 ASN A 18 -79.03 -131.40 REMARK 500 1 ASP A 52 102.76 -54.42 REMARK 500 1 CYS A 55 156.28 -47.25 REMARK 500 2 ASN A 6 44.25 -94.44 REMARK 500 2 TYR A 9 -57.42 -145.94 REMARK 500 2 CYS A 10 156.91 -47.22 REMARK 500 2 ARG A 13 69.91 63.49 REMARK 500 2 ASN A 17 43.05 -88.87 REMARK 500 2 ASN A 18 -78.66 -132.60 REMARK 500 2 CYS A 55 156.23 -47.40 REMARK 500 3 ASN A 6 43.43 -92.88 REMARK 500 3 TYR A 9 -57.21 -145.87 REMARK 500 3 CYS A 10 157.12 -47.32 REMARK 500 3 ARG A 13 69.84 63.37 REMARK 500 3 ASN A 17 43.13 -88.86 REMARK 500 3 ASN A 18 -78.75 -132.42 REMARK 500 3 CYS A 55 155.94 -46.92 REMARK 500 4 ASN A 6 49.94 -108.75 REMARK 500 4 TYR A 9 -57.02 -145.25 REMARK 500 4 CYS A 10 157.33 -47.37 REMARK 500 4 ASN A 17 43.16 -88.64 REMARK 500 4 ASN A 18 -79.09 -132.21 REMARK 500 4 ASP A 52 103.51 -53.72 REMARK 500 4 CYS A 55 155.93 -47.24 REMARK 500 5 ASN A 6 43.77 -93.47 REMARK 500 5 TYR A 9 -58.26 -146.32 REMARK 500 5 CYS A 10 156.71 -47.64 REMARK 500 5 ARG A 13 70.44 61.91 REMARK 500 5 ASN A 17 42.98 -89.11 REMARK 500 5 ASN A 18 -78.90 -132.03 REMARK 500 5 CYS A 55 155.60 -46.81 REMARK 500 6 ASN A 6 34.36 -95.77 REMARK 500 6 TYR A 9 -56.16 -145.56 REMARK 500 6 CYS A 10 157.31 -48.01 REMARK 500 6 ARG A 13 69.90 64.17 REMARK 500 6 ASN A 17 43.06 -89.49 REMARK 500 6 ASN A 18 -76.45 -135.21 REMARK 500 6 ASP A 52 105.50 -51.93 REMARK 500 6 CYS A 55 155.97 -46.98 REMARK 500 7 ASN A 6 50.67 -108.13 REMARK 500 7 TYR A 9 -57.31 -145.30 REMARK 500 7 CYS A 10 156.82 -46.89 REMARK 500 7 ARG A 13 70.03 63.38 REMARK 500 7 ASN A 17 43.36 -88.25 REMARK 500 7 ASN A 18 -79.07 -132.35 REMARK 500 REMARK 500 THIS ENTRY HAS 150 RAMACHANDRAN OUTLIERS. 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 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 10 SG REMARK 620 2 CYS A 12 SG 109.7 REMARK 620 3 HIS A 32 ND1 93.1 100.7 REMARK 620 4 CYS A 35 SG 99.1 132.2 115.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 CYS A 27 SG 103.0 REMARK 620 3 CYS A 55 SG 102.6 130.8 REMARK 620 4 CYS A 58 SG 125.7 98.9 99.1 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18963 RELATED DB: BMRB DBREF 2M3H A 4 61 UNP Q9BTC0 DIDO1_HUMAN 265 322 SEQADV 2M3H GLY A 1 UNP Q9BTC0 EXPRESSION TAG SEQADV 2M3H SER A 2 UNP Q9BTC0 EXPRESSION TAG SEQADV 2M3H MET A 3 UNP Q9BTC0 EXPRESSION TAG SEQRES 1 A 61 GLY SER MET ASP PRO ASN ALA LEU TYR CYS ILE CYS ARG SEQRES 2 A 61 GLN PRO HIS ASN ASN ARG PHE MET ILE CYS CYS ASP ARG SEQRES 3 A 61 CYS GLU GLU TRP PHE HIS GLY ASP CYS VAL GLY ILE SER SEQRES 4 A 61 GLU ALA ARG GLY ARG LEU LEU GLU ARG ASN GLY GLU ASP SEQRES 5 A 61 TYR ILE CYS PRO ASN CYS THR ILE LEU HET ZN A 101 1 HET ZN A 102 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 GLY A 33 GLY A 37 1 5 HELIX 2 2 SER A 39 GLY A 50 1 12 SHEET 1 A 2 MET A 21 CYS A 24 0 SHEET 2 A 2 GLU A 29 HIS A 32 -1 O GLU A 29 N CYS A 24 LINK SG CYS A 10 ZN ZN A 101 1555 1555 2.30 LINK SG CYS A 12 ZN ZN A 101 1555 1555 2.10 LINK SG CYS A 24 ZN ZN A 102 1555 1555 2.30 LINK SG CYS A 27 ZN ZN A 102 1555 1555 2.42 LINK ND1 HIS A 32 ZN ZN A 101 1555 1555 2.41 LINK SG CYS A 35 ZN ZN A 101 1555 1555 2.52 LINK SG CYS A 55 ZN ZN A 102 1555 1555 2.24 LINK SG CYS A 58 ZN ZN A 102 1555 1555 2.47 SITE 1 AC1 4 CYS A 10 CYS A 12 HIS A 32 CYS A 35 SITE 1 AC2 5 CYS A 24 CYS A 27 PHE A 31 CYS A 55 SITE 2 AC2 5 CYS A 58 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