HEADER METAL BINDING PROTEIN 08-NOV-10 2L5U TITLE STRUCTURE OF THE FIRST PHD FINGER (PHD1) FROM CHD4 (MI2B) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD1 DOMAIN, UNP RESIDUES 365-420; COMPND 5 SYNONYM: CHD-4, ATP-DEPENDENT HELICASE CHD4, MI-2 AUTOANTIGEN 218 KDA COMPND 6 PROTEIN, MI2-BETA; 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 GENE: CHD4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX-6PE; SOURCE 9 OTHER_DETAILS: PGEX-6PE IS AN EDITED VERSION OF PGEX-2T WHICH SOURCE 10 CONTAINS AN HRV3C PROTEASE CLEAVAGE SITE. KEYWDS CHD4, MI2B, MI2-BETA, PHD, PROTEIN BINDING, PEPTIDE BINDING PROTEIN, KEYWDS 2 METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.E.MANSFIELD,A.H.KWAN,J.P.MACKAY REVDAT 3 01-MAY-24 2L5U 1 REMARK SEQADV LINK REVDAT 2 13-APR-11 2L5U 1 JRNL REVDAT 1 19-JAN-11 2L5U 0 JRNL AUTH R.E.MANSFIELD,C.A.MUSSELMAN,A.H.KWAN,S.S.OLIVER,A.L.GARSKE, JRNL AUTH 2 F.DAVRAZOU,J.M.DENU,T.G.KUTATELADZE,J.P.MACKAY JRNL TITL PLANT HOMEODOMAIN (PHD) FINGERS OF CHD4 ARE HISTONE JRNL TITL 2 H3-BINDING MODULES WITH PREFERENCE FOR UNMODIFIED H3K4 AND JRNL TITL 3 METHYLATED H3K9 JRNL REF J.BIOL.CHEM. V. 286 11779 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21278251 JRNL DOI 10.1074/JBC.M110.208207 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, ARIA 1.2 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), LINGE, O'DONOGHUE AND REMARK 3 NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE CALCULATIONS WERE PERFORMED REMARK 3 USING THE PACKAGE ARIA1.2. FINAL STRUCTURES ARE BASED ON 988 NOE- REMARK 3 DERIVED DISTANCE CONSTRAINTS AND 79 ADDITIONAL DIHEDRAL ANGLE REMARK 3 RESTRAINTS. REMARK 4 REMARK 4 2L5U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000101994. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 60 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7 MM [U-100% 13C; U-100% 15N] REMARK 210 CHD4 PHD1-1, 10 MM SODIUM REMARK 210 PHOSPHATE-2, 50 MM SODIUM REMARK 210 CHLORIDE-3, 1 MM DTT-4, 20 UM REMARK 210 DSS-5, 93% H2O/7% D2O; 1 MM CHD4 REMARK 210 PHD1-6, 10 MM SODIUM PHOSPHATE-7, REMARK 210 50 MM SODIUM CHLORIDE-8, 1 MM REMARK 210 DTT-9, 20 UM DSS-10, 93% H2O/7% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-15N HSQC; REMARK 210 2D 1H-13C HSQC; 3D HNCA; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D HNHA; REMARK 210 3D HBHA(CO)NH; 3D HNCO; 3D HN(CA) REMARK 210 CO; 3D HCCH-TOCSY; 3D HNHB; 2D REMARK 210 (HB)CB(CGCD)HD; 2D (HB)CB(CGCDCE) REMARK 210 HE; 3D 1H-15N NOESY; 2D 1H-1H REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, ARIA 1.2, TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 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 HZ3 LYS A 44 OE1 GLU A 47 1.57 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 GLU A 7 -73.33 -68.54 REMARK 500 1 PRO A 30 24.63 -78.14 REMARK 500 1 ASP A 39 118.94 -172.01 REMARK 500 1 ILE A 60 51.27 -90.63 REMARK 500 2 PRO A 2 48.10 -76.04 REMARK 500 3 SER A 5 45.82 -76.59 REMARK 500 3 TYR A 6 -75.09 -150.41 REMARK 500 3 THR A 8 -148.20 48.24 REMARK 500 3 GLN A 18 74.72 63.71 REMARK 500 3 GLN A 19 -148.18 78.42 REMARK 500 3 PRO A 30 33.21 -81.49 REMARK 500 4 ASP A 39 101.73 -177.56 REMARK 500 4 PRO A 40 26.66 -70.52 REMARK 500 4 GLU A 43 -95.37 -136.50 REMARK 500 4 PRO A 46 45.65 -73.96 REMARK 500 4 ILE A 60 33.78 -83.65 REMARK 500 5 PRO A 2 96.50 -69.13 REMARK 500 5 GLU A 7 -89.70 176.78 REMARK 500 5 PRO A 30 31.82 -77.52 REMARK 500 5 ASP A 39 93.41 -165.55 REMARK 500 6 GLU A 7 -107.55 64.27 REMARK 500 6 GLU A 22 46.92 -82.76 REMARK 500 6 ASP A 39 133.76 -178.60 REMARK 500 6 ASP A 41 55.66 -94.32 REMARK 500 6 PRO A 46 34.63 -77.76 REMARK 500 6 ILE A 60 58.94 -99.25 REMARK 500 7 GLU A 7 -84.76 -116.20 REMARK 500 7 ASP A 39 98.01 -170.24 REMARK 500 7 GLU A 43 -74.76 -145.32 REMARK 500 7 GLU A 47 59.51 -90.76 REMARK 500 8 TYR A 6 -82.93 -102.87 REMARK 500 8 GLU A 7 -100.17 -148.35 REMARK 500 9 LEU A 3 -44.77 -144.37 REMARK 500 9 GLU A 7 -75.08 69.12 REMARK 500 9 GLN A 19 -165.36 -105.66 REMARK 500 10 GLN A 19 118.60 -170.07 REMARK 500 10 ASP A 41 56.24 -154.80 REMARK 500 10 GLU A 43 55.44 -93.80 REMARK 500 11 ASP A 39 108.21 -162.52 REMARK 500 11 ASP A 41 -36.45 -141.32 REMARK 500 11 GLU A 43 -55.62 -141.93 REMARK 500 12 SER A 5 46.42 -85.15 REMARK 500 12 TYR A 6 144.62 -170.47 REMARK 500 12 GLU A 7 -67.33 -107.27 REMARK 500 12 GLN A 19 -74.63 -116.63 REMARK 500 12 ASP A 39 106.59 -162.49 REMARK 500 13 TYR A 6 -115.09 -118.33 REMARK 500 13 PRO A 30 38.69 -79.81 REMARK 500 13 ASP A 39 125.11 -176.89 REMARK 500 13 GLU A 43 -73.84 -136.56 REMARK 500 REMARK 500 THIS ENTRY HAS 86 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 63 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 14 SG REMARK 620 2 CYS A 17 SG 109.4 REMARK 620 3 HIS A 34 ND1 107.2 110.1 REMARK 620 4 CYS A 37 SG 111.1 110.9 107.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 62 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 26 SG REMARK 620 2 CYS A 29 SG 110.0 REMARK 620 3 CYS A 52 SG 111.8 108.4 REMARK 620 4 CYS A 55 SG 107.6 107.7 111.3 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 62 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 63 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17285 RELATED DB: BMRB DBREF 2L5U A 6 61 UNP Q14839 CHD4_HUMAN 365 420 SEQADV 2L5U GLY A 1 UNP Q14839 EXPRESSION TAG SEQADV 2L5U PRO A 2 UNP Q14839 EXPRESSION TAG SEQADV 2L5U LEU A 3 UNP Q14839 EXPRESSION TAG SEQADV 2L5U GLY A 4 UNP Q14839 EXPRESSION TAG SEQADV 2L5U SER A 5 UNP Q14839 EXPRESSION TAG SEQRES 1 A 61 GLY PRO LEU GLY SER TYR GLU THR ASP HIS GLN ASP TYR SEQRES 2 A 61 CYS GLU VAL CYS GLN GLN GLY GLY GLU ILE ILE LEU CYS SEQRES 3 A 61 ASP THR CYS PRO ARG ALA TYR HIS MET VAL CYS LEU ASP SEQRES 4 A 61 PRO ASP MET GLU LYS ALA PRO GLU GLY LYS TRP SER CYS SEQRES 5 A 61 PRO HIS CYS GLU LYS GLU GLY ILE GLN HET ZN A 62 1 HET ZN A 63 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 HIS A 34 ASP A 39 1 6 HELIX 2 2 HIS A 54 GLY A 59 5 6 SHEET 1 A 2 ILE A 24 LEU A 25 0 SHEET 2 A 2 ALA A 32 TYR A 33 -1 O TYR A 33 N ILE A 24 LINK SG CYS A 14 ZN ZN A 63 1555 1555 2.27 LINK SG CYS A 17 ZN ZN A 63 1555 1555 2.28 LINK SG CYS A 26 ZN ZN A 62 1555 1555 2.32 LINK SG CYS A 29 ZN ZN A 62 1555 1555 2.27 LINK ND1 HIS A 34 ZN ZN A 63 1555 1555 1.99 LINK SG CYS A 37 ZN ZN A 63 1555 1555 2.25 LINK SG CYS A 52 ZN ZN A 62 1555 1555 2.31 LINK SG CYS A 55 ZN ZN A 62 1555 1555 2.30 SITE 1 AC1 5 CYS A 26 THR A 28 CYS A 29 CYS A 52 SITE 2 AC1 5 CYS A 55 SITE 1 AC2 4 CYS A 14 CYS A 17 HIS A 34 CYS A 37 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