HEADER DNA BINDING PROTEIN 02-SEP-02 1MM2 TITLE SOLUTION STRUCTURE OF THE 2ND PHD DOMAIN FROM MI2B COMPND MOL_ID: 1; COMPND 2 MOLECULE: MI2-BETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MI2-BETA (RESIDUES 446-501); COMPND 5 SYNONYM: CHROMODOMAIN HELICASE-DNA-BINDING PROTEIN 4; 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: CHD4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P KEYWDS PHD, ZINC FINGER, PROTEIN SCAFFOLD, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.H.Y.KWAN,D.A.GELL,A.VERGER,M.CROSSLEY,J.M.MATTHEWS,J.P.MACKAY REVDAT 3 23-FEB-22 1MM2 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1MM2 1 VERSN REVDAT 1 22-JUL-03 1MM2 0 JRNL AUTH A.H.Y.KWAN,D.A.GELL,A.VERGER,M.CROSSLEY,J.M.MATTHEWS, JRNL AUTH 2 J.P.MACKAY JRNL TITL ENGINEERING A PROTEIN SCAFFOLD FROM A PHD FINGER JRNL REF STRUCTURE V. 11 803 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 12842043 JRNL DOI 10.1016/S0969-2126(03)00122-9 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.5, DYANA 1.5 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT ET AL (DYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE CALCULATIONS WERE PERFORMED REMARK 3 USING THE PACKAGE ARIA1.1 (AMBIGUOUS RESTRAINTS IN ITERATIVE REMARK 3 ASSIGNMENT). FINAL STRUCTURES ARE BASED ON 1284 UNAMBIGUOUS NOE- REMARK 3 DERIVED DISTANCE CONSTRAINTS, 8 SETS OF AMBIGUOUS NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS AND 39 ADDITIONAL DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1MM2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-SEP-02. REMARK 100 THE DEPOSITION ID IS D_1000017008. 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 : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM MI2-PHD2 PROTEIN, 1MM DTT, REMARK 210 10MM SODIUM PHOSPHATE BUFFER (PH REMARK 210 7.5), 150MM NACL, 95% H2O, 5% REMARK 210 D2O; 0.2MM N15-LABELLED MI2-PHD2 REMARK 210 PROTEIN, 1MM DTT, 10MM SODIUM REMARK 210 PHOSPHATE BUFFER (PH 7.5), 150MM REMARK 210 NACL, 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; REMARK 210 N15-HSQC 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 : XEASY 1.3.13, ARIA 1.1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS, TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 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: THIS STRUCTURE WAS DETERMINED MOSTLY USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES 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 HG CYS A 12 ZN ZN A 63 1.06 REMARK 500 HB2 CYS A 24 HB3 CYS A 50 1.28 REMARK 500 HB2 ARG A 52 HB3 LEU A 58 1.30 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 ASP A 6 -169.78 -171.67 REMARK 500 1 HIS A 8 -131.40 62.66 REMARK 500 1 VAL A 14 -62.07 -99.88 REMARK 500 1 PRO A 28 38.18 -75.32 REMARK 500 1 TYR A 31 -146.52 -117.20 REMARK 500 1 PRO A 51 10.41 -69.91 REMARK 500 1 PRO A 56 44.18 -79.17 REMARK 500 1 ALA A 57 -163.65 -162.72 REMARK 500 2 ASP A 6 -132.89 -89.40 REMARK 500 2 THR A 26 -61.58 -106.08 REMARK 500 2 TYR A 31 -161.51 -127.33 REMARK 500 2 HIS A 32 -130.25 -123.07 REMARK 500 2 HIS A 34 -3.14 -143.46 REMARK 500 2 CYS A 50 159.85 -48.51 REMARK 500 2 ALA A 57 46.33 -109.16 REMARK 500 3 PRO A 28 40.79 -81.56 REMARK 500 3 TYR A 31 -153.43 -131.44 REMARK 500 3 LEU A 36 -166.57 -125.72 REMARK 500 3 CYS A 50 159.32 -46.92 REMARK 500 3 PRO A 51 34.57 -66.30 REMARK 500 3 ARG A 52 -47.18 -141.75 REMARK 500 3 CYS A 55 71.41 53.30 REMARK 500 4 LEU A 3 -74.55 67.95 REMARK 500 4 SER A 5 48.98 -95.65 REMARK 500 4 CYS A 12 -109.06 48.16 REMARK 500 4 ARG A 13 -55.00 -179.06 REMARK 500 4 ASP A 17 -138.72 168.31 REMARK 500 4 HIS A 32 -125.08 -128.96 REMARK 500 4 LYS A 59 106.75 -165.27 REMARK 500 5 HIS A 7 -67.36 70.34 REMARK 500 5 PRO A 28 34.29 -82.46 REMARK 500 5 TYR A 31 -152.95 -130.87 REMARK 500 5 HIS A 32 -138.17 -134.38 REMARK 500 5 PRO A 51 13.76 -66.99 REMARK 500 5 ALA A 57 32.93 -143.73 REMARK 500 5 LYS A 59 29.54 -147.06 REMARK 500 6 HIS A 8 -102.30 68.68 REMARK 500 6 PRO A 28 48.33 -88.22 REMARK 500 6 TYR A 31 -159.64 -133.35 REMARK 500 6 LEU A 36 -166.21 -118.13 REMARK 500 6 PRO A 51 42.25 -66.46 REMARK 500 6 ARG A 52 -29.79 -151.29 REMARK 500 6 CYS A 55 146.22 74.22 REMARK 500 7 SER A 5 -68.51 -95.45 REMARK 500 7 HIS A 8 -120.07 62.79 REMARK 500 7 VAL A 14 -47.92 -138.22 REMARK 500 7 TYR A 31 -162.10 -128.80 REMARK 500 7 GLU A 47 59.98 -99.73 REMARK 500 7 PRO A 51 16.02 -68.03 REMARK 500 8 LEU A 3 -164.88 64.58 REMARK 500 REMARK 500 THIS ENTRY HAS 148 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 12 SG REMARK 620 2 CYS A 15 SG 108.5 REMARK 620 3 HIS A 32 ND1 109.0 108.5 REMARK 620 4 CYS A 35 SG 111.3 109.4 110.1 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 24 SG REMARK 620 2 CYS A 27 SG 109.3 REMARK 620 3 CYS A 50 SG 111.8 108.8 REMARK 620 4 CYS A 53 SG 109.4 107.8 109.6 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: 1FP0 RELATED DB: PDB REMARK 900 1FP0 CONTAINS PHD DOMAIN FROM KAP-1 REMARK 900 RELATED ID: 1F62 RELATED DB: PDB REMARK 900 1F62 CONTAINS PHD DOMAIN FROM WSTF REMARK 900 RELATED ID: 1MM3 RELATED DB: PDB REMARK 900 1MM3 CONTAINS THE 2ND PHD DOMAIN FROM MI2B WITH C-TERMINAL LOOP REMARK 900 REPLACED BY CORRESPONDING LOOP FROM WSTF DBREF 1MM2 A 6 61 UNP Q14839 CHD4_HUMAN 446 501 SEQADV 1MM2 GLY A 1 UNP Q14839 CLONING ARTIFACT SEQADV 1MM2 PRO A 2 UNP Q14839 CLONING ARTIFACT SEQADV 1MM2 LEU A 3 UNP Q14839 CLONING ARTIFACT SEQADV 1MM2 GLY A 4 UNP Q14839 CLONING ARTIFACT SEQADV 1MM2 SER A 5 UNP Q14839 CLONING ARTIFACT SEQRES 1 A 61 GLY PRO LEU GLY SER ASP HIS HIS MET GLU PHE CYS ARG SEQRES 2 A 61 VAL CYS LYS ASP GLY GLY GLU LEU LEU CYS CYS ASP THR SEQRES 3 A 61 CYS PRO SER SER TYR HIS ILE HIS CYS LEU ASN PRO PRO SEQRES 4 A 61 LEU PRO GLU ILE PRO ASN GLY GLU TRP LEU CYS PRO ARG SEQRES 5 A 61 CYS THR CYS PRO ALA LEU LYS GLY LYS HET ZN A 62 1 HET ZN A 63 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) LINK SG CYS A 12 ZN ZN A 63 1555 1555 2.24 LINK SG CYS A 15 ZN ZN A 63 1555 1555 2.29 LINK SG CYS A 24 ZN ZN A 62 1555 1555 2.32 LINK SG CYS A 27 ZN ZN A 62 1555 1555 2.27 LINK ND1 HIS A 32 ZN ZN A 63 1555 1555 1.96 LINK SG CYS A 35 ZN ZN A 63 1555 1555 2.33 LINK SG CYS A 50 ZN ZN A 62 1555 1555 2.29 LINK SG CYS A 53 ZN ZN A 62 1555 1555 2.28 SITE 1 AC1 4 CYS A 24 CYS A 27 CYS A 50 CYS A 53 SITE 1 AC2 4 CYS A 12 CYS A 15 HIS A 32 CYS A 35 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