10 20 30 40 50 60 70 80 1WEM - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA BINDING PROTEIN 25-MAY-04 1WEM
TITLE SOLUTION STRUCTURE OF PHD DOMAIN IN DEATH INDUCER- TITLE 2 OBLITERATOR 1(DIO-1)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEATH ASSOCIATED TRANSCRIPTION FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD DOMAIN; COMPND 5 SYNONYM: DEATH INDUCER-OBLITERATOR-1, DIO-1; COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RIKEN CDNA 3830408B01; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P030421-56; SOURCE 8 OTHER_DETAILS: CELL FREE PROTEIN SYNTHESIS
KEYWDS NMR, STRUCTURAL GENOMICS, PHD DOMAIN, DEATH INDUCER- KEYWDS 2 OBLITERATOR 1(DIO-1), RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 3 INITIATIVE, RSGI, DNA BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR F.HE,Y.MUTO,M.INOUE,T.KIGAWA,M.SHIROUZU,T.TERADA,S.YOKOYAMA, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 2 24-FEB-09 1WEM 1 VERSN REVDAT 1 25-NOV-04 1WEM 0
JRNL AUTH F.HE,Y.MUTO,M.INOUE,T.KIGAWA,M.SHIROUZU,T.TERADA, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF PHD DOMAIN IN DEATH JRNL TITL 2 INDUCER-OBLITERATOR 1(DIO-1) JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.0.17 REMARK 3 AUTHORS : GUENTERT,P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1WEM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAY-04. REMARK 100 THE RCSB ID CODE IS RCSB023494.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8MM U-15, 13C; 20MM D-TRIS- REMARK 210 HCL(PH 7.0); 100MM NACL; 0.1MM REMARK 210 ZNCL2; 1MM D-DTT; 0.02% NAN3; REMARK 210 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, NMRPIPE REMARK 210 20020425, NMRVIEW 5.0.5, REMARK 210 KUJIRA 0.863, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY, 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 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 SER A 2 123.49 -35.57 REMARK 500 1 GLU A 8 150.70 -47.13 REMARK 500 1 ASP A 13 116.79 -38.65 REMARK 500 1 TYR A 18 -74.93 -117.71 REMARK 500 1 ASN A 27 -36.75 -35.30 REMARK 500 1 ARG A 28 147.60 -39.45 REMARK 500 1 ILE A 47 122.49 -37.32 REMARK 500 1 CYS A 64 156.77 -41.86 REMARK 500 1 SER A 74 175.36 -50.55 REMARK 500 2 VAL A 11 -27.79 -37.83 REMARK 500 2 ASP A 13 108.60 -55.39 REMARK 500 2 TYR A 18 -62.49 -123.41 REMARK 500 2 PRO A 24 -173.05 -69.82 REMARK 500 2 ARG A 28 149.47 -34.57 REMARK 500 2 CYS A 33 161.25 -40.27 REMARK 500 2 ILE A 47 142.72 -37.81 REMARK 500 2 LEU A 55 -32.47 -34.61 REMARK 500 2 CYS A 64 155.58 -39.05 REMARK 500 2 ILE A 69 -39.02 -35.53 REMARK 500 2 SER A 74 43.77 -81.64 REMARK 500 3 SER A 5 174.27 -58.34 REMARK 500 3 SER A 6 -57.65 -127.32 REMARK 500 3 TYR A 18 -66.90 -127.58 REMARK 500 3 ARG A 28 151.95 -37.50 REMARK 500 3 LEU A 55 -27.47 -37.89 REMARK 500 3 CYS A 64 156.77 -39.60 REMARK 500 4 CYS A 9 123.68 -36.51 REMARK 500 4 TYR A 12 178.57 -56.06 REMARK 500 4 TYR A 18 -67.27 -130.29 REMARK 500 4 ASN A 26 -174.54 -66.58 REMARK 500 4 ASN A 27 42.14 -80.23 REMARK 500 4 ILE A 47 150.54 -35.82 REMARK 500 4 LEU A 55 -25.77 -38.67 REMARK 500 4 GLU A 56 -71.25 -86.68 REMARK 500 4 ILE A 63 97.08 -46.61 REMARK 500 4 CYS A 64 156.50 -37.75 REMARK 500 4 PRO A 73 87.20 -69.81 REMARK 500 5 SER A 5 106.81 -167.56 REMARK 500 5 VAL A 11 45.78 -80.66 REMARK 500 5 PRO A 24 -171.51 -69.77 REMARK 500 5 ARG A 28 148.48 -33.51 REMARK 500 5 CYS A 33 170.18 -51.15 REMARK 500 5 LEU A 55 -31.05 -36.68 REMARK 500 5 CYS A 64 157.57 -38.48 REMARK 500 6 TYR A 18 -75.41 -92.10 REMARK 500 6 CYS A 19 168.09 -48.40 REMARK 500 6 ASN A 27 -36.81 -38.44 REMARK 500 6 ARG A 28 153.53 -42.18 REMARK 500 6 ILE A 47 135.32 -35.87 REMARK 500 6 LEU A 55 -25.37 -39.53 REMARK 500 6 CYS A 64 159.12 -45.67 REMARK 500 6 ILE A 69 -39.12 -37.91 REMARK 500 7 GLU A 8 151.59 -47.71 REMARK 500 7 VAL A 11 124.50 -173.99 REMARK 500 7 TYR A 18 -65.43 -91.39 REMARK 500 7 PRO A 24 -174.47 -69.83 REMARK 500 7 ARG A 28 146.57 -36.64 REMARK 500 7 ILE A 47 149.35 -38.03 REMARK 500 7 CYS A 64 156.40 -38.32 REMARK 500 7 CYS A 67 -71.99 -77.92 REMARK 500 7 SER A 74 83.91 -67.36 REMARK 500 8 TYR A 12 -44.56 -130.67 REMARK 500 8 TYR A 18 -63.08 -132.06 REMARK 500 8 PRO A 24 -173.50 -69.78 REMARK 500 8 ASN A 26 -72.70 -78.76 REMARK 500 8 ASN A 27 -33.27 -132.16 REMARK 500 8 ARG A 28 138.21 -34.66 REMARK 500 8 ILE A 47 122.37 -37.22 REMARK 500 8 LEU A 55 -32.33 -34.80 REMARK 500 8 GLU A 56 -70.59 -64.01 REMARK 500 8 CYS A 64 156.54 -38.56 REMARK 500 8 ILE A 69 -26.27 -40.00 REMARK 500 8 SER A 71 -74.99 -117.19 REMARK 500 9 ASP A 13 128.81 -38.76 REMARK 500 9 PRO A 24 -174.39 -69.74 REMARK 500 9 ARG A 28 147.50 -34.24 REMARK 500 9 CYS A 33 167.68 -43.48 REMARK 500 9 ILE A 47 148.47 -35.23 REMARK 500 9 LEU A 55 -38.26 -39.42 REMARK 500 9 GLU A 56 -70.93 -55.83 REMARK 500 9 CYS A 64 157.37 -40.32 REMARK 500 10 SER A 2 108.81 -164.36 REMARK 500 10 GLU A 8 106.08 -56.80 REMARK 500 10 VAL A 11 32.71 34.05 REMARK 500 10 PRO A 24 -173.85 -69.77 REMARK 500 10 ARG A 28 147.72 -34.58 REMARK 500 10 LEU A 55 -34.42 -34.69 REMARK 500 10 CYS A 64 155.93 -41.48 REMARK 500 11 TYR A 18 -74.82 -131.42 REMARK 500 11 CYS A 19 162.84 -47.85 REMARK 500 11 ARG A 28 145.87 -36.53 REMARK 500 11 ILE A 47 150.84 -36.46 REMARK 500 11 GLU A 56 -70.76 -72.12 REMARK 500 11 CYS A 64 158.37 -41.07 REMARK 500 11 CYS A 67 -71.78 -77.39 REMARK 500 12 CYS A 9 36.79 73.10 REMARK 500 12 TYR A 12 107.94 -46.75 REMARK 500 12 ASP A 13 118.71 -162.05 REMARK 500 12 TYR A 18 -74.99 -132.90 REMARK 500 12 PRO A 24 -173.33 -69.74 REMARK 500 12 ARG A 35 -64.17 -92.15 REMARK 500 12 ILE A 47 128.42 -38.95 REMARK 500 12 GLU A 56 -70.95 -79.79 REMARK 500 12 CYS A 64 157.04 -46.70 REMARK 500 12 PRO A 73 87.53 -69.70 REMARK 500 13 ASN A 27 -39.33 -37.81 REMARK 500 13 ARG A 28 141.94 -37.03 REMARK 500 13 ILE A 47 124.86 -39.20 REMARK 500 13 CYS A 64 156.08 -42.33 REMARK 500 13 CYS A 67 -71.12 -78.10 REMARK 500 14 CYS A 9 134.64 -35.89 REMARK 500 14 TYR A 12 -62.16 -94.83 REMARK 500 14 TYR A 18 -74.38 -132.59 REMARK 500 14 CYS A 19 165.38 -48.81 REMARK 500 14 ARG A 28 153.26 -35.62 REMARK 500 14 ILE A 47 130.51 -34.59 REMARK 500 14 CYS A 64 156.86 -39.92 REMARK 500 14 ILE A 69 -37.61 -35.50 REMARK 500 15 ASP A 13 103.08 -42.71 REMARK 500 15 ASN A 15 41.66 -109.90 REMARK 500 15 TYR A 18 -73.81 -100.91 REMARK 500 15 CYS A 19 171.42 -52.67 REMARK 500 15 PRO A 24 -174.73 -69.79 REMARK 500 15 GLU A 56 -70.82 -85.33 REMARK 500 15 CYS A 64 156.36 -40.55 REMARK 500 15 ASN A 66 -31.68 -39.31 REMARK 500 15 PRO A 73 2.74 -69.75 REMARK 500 16 VAL A 11 37.29 -84.10 REMARK 500 16 TYR A 18 -72.95 -132.88 REMARK 500 16 ARG A 28 149.83 -33.64 REMARK 500 16 ILE A 47 132.75 -34.64 REMARK 500 16 GLU A 56 -71.08 -85.24 REMARK 500 16 CYS A 64 159.26 -41.48 REMARK 500 16 LEU A 70 -75.16 -70.27 REMARK 500 16 SER A 71 -71.47 -90.98 REMARK 500 16 SER A 75 -63.79 -98.36 REMARK 500 17 SER A 2 42.18 -83.43 REMARK 500 17 CYS A 9 98.73 -44.88 REMARK 500 17 PRO A 14 1.94 -69.77 REMARK 500 17 TYR A 18 -74.52 -129.81 REMARK 500 17 PRO A 24 -165.31 -69.71 REMARK 500 17 HIS A 25 73.44 -110.24 REMARK 500 17 LEU A 55 -28.76 -36.96 REMARK 500 17 GLU A 56 -70.99 -88.93 REMARK 500 17 CYS A 64 156.87 -40.36 REMARK 500 17 CYS A 67 -70.01 -75.16 REMARK 500 17 SER A 71 47.73 -85.59 REMARK 500 17 PRO A 73 3.72 -69.75 REMARK 500 17 SER A 74 120.67 -34.35 REMARK 500 18 GLU A 10 165.96 -43.13 REMARK 500 18 TYR A 12 46.67 34.04 REMARK 500 18 PRO A 24 -172.44 -69.79 REMARK 500 18 ASN A 26 -72.03 -92.62 REMARK 500 18 ASN A 27 -31.72 -131.87 REMARK 500 18 ARG A 28 139.38 -36.94 REMARK 500 18 ILE A 47 149.20 -35.99 REMARK 500 18 LEU A 55 -28.78 -38.25 REMARK 500 18 GLU A 56 -71.03 -80.14 REMARK 500 18 CYS A 64 158.15 -39.14 REMARK 500 19 CYS A 9 155.74 -49.96 REMARK 500 19 TYR A 18 -60.77 -123.97 REMARK 500 19 PRO A 24 -179.39 -69.76 REMARK 500 19 ARG A 28 149.80 -34.71 REMARK 500 19 ILE A 47 139.27 -34.37 REMARK 500 19 LEU A 55 -35.04 -33.14 REMARK 500 19 CYS A 64 157.56 -38.35 REMARK 500 19 ILE A 69 -35.67 -36.15 REMARK 500 19 PRO A 73 1.04 -69.73 REMARK 500 20 SER A 3 -57.37 -131.36 REMARK 500 20 PRO A 24 -177.70 -69.74 REMARK 500 20 ARG A 28 147.11 -33.77 REMARK 500 20 ILE A 47 145.46 -37.44 REMARK 500 20 LEU A 55 -27.36 -37.98 REMARK 500 20 ASP A 61 97.59 -64.21 REMARK 500 20 CYS A 64 157.34 -41.16 REMARK 500 20 PRO A 73 0.57 -69.74 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 19 SG REMARK 620 2 HIS A 41 ND1 100.7 REMARK 620 3 CYS A 44 SG 118.1 113.7 REMARK 620 4 CYS A 21 SG 100.7 102.9 118.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 36 SG REMARK 620 2 CYS A 67 SG 95.1 REMARK 620 3 CYS A 33 SG 114.6 118.1 REMARK 620 4 CYS A 64 SG 117.7 94.2 114.2 REMARK 620 N 1 2 3
REMARK 650 REMARK 650 HELIX REMARK 650 AUTHOR DETERMINATION METHOD: AUTHOR DETERMINED
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 201 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MMT007015491.1 RELATED DB: TARGETDB
DBREF 1WEM A 8 70 UNP Q8C9B9 DIDO1_MOUSE 257 319
SEQADV 1WEM GLY A 1 UNP Q8C9B9 CLONING ARTIFACT SEQADV 1WEM SER A 2 UNP Q8C9B9 CLONING ARTIFACT SEQADV 1WEM SER A 3 UNP Q8C9B9 CLONING ARTIFACT SEQADV 1WEM GLY A 4 UNP Q8C9B9 CLONING ARTIFACT SEQADV 1WEM SER A 5 UNP Q8C9B9 CLONING ARTIFACT SEQADV 1WEM SER A 6 UNP Q8C9B9 CLONING ARTIFACT SEQADV 1WEM GLY A 7 UNP Q8C9B9 CLONING ARTIFACT SEQADV 1WEM SER A 71 UNP Q8C9B9 CLONING ARTIFACT SEQADV 1WEM GLY A 72 UNP Q8C9B9 CLONING ARTIFACT SEQADV 1WEM PRO A 73 UNP Q8C9B9 CLONING ARTIFACT SEQADV 1WEM SER A 74 UNP Q8C9B9 CLONING ARTIFACT SEQADV 1WEM SER A 75 UNP Q8C9B9 CLONING ARTIFACT SEQADV 1WEM GLY A 76 UNP Q8C9B9 CLONING ARTIFACT
SEQRES 1 A 76 GLY SER SER GLY SER SER GLY GLU CYS GLU VAL TYR ASP SEQRES 2 A 76 PRO ASN ALA LEU TYR CYS ILE CYS ARG GLN PRO HIS ASN SEQRES 3 A 76 ASN ARG PHE MET ILE CYS CYS ASP ARG CYS GLU GLU TRP SEQRES 4 A 76 PHE HIS GLY ASP CYS VAL GLY ILE SER GLU ALA ARG GLY SEQRES 5 A 76 ARG LEU LEU GLU ARG ASN GLY GLU ASP TYR ILE CYS PRO SEQRES 6 A 76 ASN CYS THR ILE LEU SER GLY PRO SER SER GLY
HET ZN A 201 1 HET ZN A 401 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 2(ZN 2+)
HELIX 1 1 GLY A 42 VAL A 45 1 4 HELIX 2 2 GLU A 49 ASN A 58 1 10 HELIX 3 3 PRO A 65 LEU A 70 1 6
SHEET 1 A 2 MET A 30 CYS A 32 0 SHEET 2 A 2 TRP A 39 HIS A 41 -1 O PHE A 40 N ILE A 31
LINK ZN ZN A 201 SG CYS A 19 1555 1555 2.34 LINK ZN ZN A 201 ND1 HIS A 41 1555 1555 2.34 LINK ZN ZN A 201 SG CYS A 44 1555 1555 2.33 LINK ZN ZN A 201 SG CYS A 21 1555 1555 2.33 LINK ZN ZN A 401 SG CYS A 36 1555 1555 2.33 LINK ZN ZN A 401 SG CYS A 67 1555 1555 2.33 LINK ZN ZN A 401 SG CYS A 33 1555 1555 2.34 LINK ZN ZN A 401 SG CYS A 64 1555 1555 2.34
SITE 1 AC1 4 CYS A 19 CYS A 21 HIS A 41 CYS A 44 SITE 1 AC2 4 CYS A 33 CYS A 36 CYS A 64 CYS A 67
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