10 20 30 40 50 60 70 80 1MM2 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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, AUTHOR 2 J.P.MACKAY
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, JRNL AUTH 2 J.M.MATTHEWS,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 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5 REMARK 3 AUTHORS : GUNTERT ET AL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE CALCULATIONS WERE REMARK 3 PERFORMED USING THE PACKAGE ARIA1.1 (AMBIGUOUS RESTRAINTS IN REMARK 3 ITERATIVE ASSIGNMENT). FINAL STRUCTURES ARE BASED ON 1284 REMARK 3 UNAMBIGUOUS NOE-DERIVED DISTANCE CONSTRAINTS, 8 SETS OF REMARK 3 AMBIGUOUS NOE-DERIVED DISTANCE CONSTRAINTS AND 39 ADDITIONAL REMARK 3 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 RCSB ID CODE IS RCSB017008.
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 REMARK 210 DTT, 10MM SODIUM PHOSPHATE REMARK 210 BUFFER (PH 7.5), 150MM NACL, REMARK 210 95% H2O, 5% D2O; 0.2MM N15- REMARK 210 LABELLED MI2-PHD2 PROTEIN, 1MM REMARK 210 DTT, 10MM SODIUM PHOSPHATE REMARK 210 BUFFER (PH 7.5), 150MM NACL, REMARK 210 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 : XWINNMR 2.5, XEASY 1.3.13, REMARK 210 ARIA 1.1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 MOLECULAR DYNAMICS, TORSION REMARK 210 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 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 8 SER A 5 -45.95 -140.79 REMARK 500 8 ASP A 6 -138.85 -172.79 REMARK 500 8 HIS A 8 -175.84 70.93 REMARK 500 8 THR A 26 -54.00 -121.57 REMARK 500 8 PRO A 28 48.42 -78.36 REMARK 500 8 TYR A 31 -156.15 -124.87 REMARK 500 8 LEU A 36 -166.45 -123.32 REMARK 500 8 THR A 54 -78.42 -63.25 REMARK 500 9 SER A 5 -76.91 -85.14 REMARK 500 9 ASP A 6 -91.63 -150.99 REMARK 500 9 HIS A 8 -129.79 55.97 REMARK 500 9 VAL A 14 -65.92 -103.51 REMARK 500 9 PRO A 28 38.26 -74.87 REMARK 500 9 TYR A 31 -152.41 -117.02 REMARK 500 9 HIS A 32 -160.46 -129.77 REMARK 500 9 CYS A 50 158.63 -40.36 REMARK 500 10 HIS A 7 -44.52 -152.07 REMARK 500 10 HIS A 8 -137.46 50.39 REMARK 500 10 THR A 26 -63.77 -120.93 REMARK 500 10 PRO A 28 30.84 -96.36 REMARK 500 10 LEU A 36 -158.54 -116.06 REMARK 500 10 PRO A 51 37.95 -67.57 REMARK 500 10 ARG A 52 -45.17 -146.66 REMARK 500 10 THR A 54 74.31 -65.06 REMARK 500 10 CYS A 55 133.22 -175.90 REMARK 500 11 ASP A 6 -148.78 -115.16 REMARK 500 11 HIS A 7 -136.77 61.26 REMARK 500 11 VAL A 14 -49.55 -144.36 REMARK 500 11 LYS A 16 -0.97 75.14 REMARK 500 11 THR A 26 -52.52 -124.48 REMARK 500 11 TYR A 31 -161.52 -125.70 REMARK 500 11 HIS A 32 -146.28 -134.35 REMARK 500 11 PRO A 44 93.97 -67.38 REMARK 500 11 PRO A 51 34.87 -70.46 REMARK 500 11 ARG A 52 -48.66 -140.38 REMARK 500 11 CYS A 55 85.99 -160.92 REMARK 500 11 LEU A 58 -51.39 -121.50 REMARK 500 11 LYS A 59 54.44 -146.17 REMARK 500 12 HIS A 7 11.14 -147.62 REMARK 500 12 PRO A 28 32.51 -92.32 REMARK 500 12 HIS A 32 -133.30 -126.07 REMARK 500 12 CYS A 55 101.36 65.24 REMARK 500 12 PRO A 56 -76.01 -66.83 REMARK 500 13 HIS A 7 -55.23 -167.47 REMARK 500 13 PRO A 28 33.06 -89.03 REMARK 500 13 TYR A 31 -154.31 -127.04 REMARK 500 13 LEU A 36 -164.16 -105.69 REMARK 500 13 LEU A 49 130.39 69.08 REMARK 500 14 TYR A 31 -155.33 -129.23 REMARK 500 14 CYS A 50 155.07 -42.00 REMARK 500 15 LEU A 3 -69.68 69.83 REMARK 500 15 ASP A 6 -72.72 -119.80 REMARK 500 15 HIS A 7 -110.71 56.05 REMARK 500 15 PRO A 28 40.47 -95.27 REMARK 500 15 TYR A 31 -166.51 -129.72 REMARK 500 15 HIS A 32 -127.73 -120.59 REMARK 500 15 PRO A 51 33.57 -70.23 REMARK 500 15 ARG A 52 -36.29 -137.56 REMARK 500 15 CYS A 55 114.38 73.79 REMARK 500 16 ASP A 6 -60.08 -96.19 REMARK 500 16 HIS A 7 97.60 65.06 REMARK 500 16 HIS A 8 -124.64 63.58 REMARK 500 16 ARG A 13 46.81 -75.49 REMARK 500 16 VAL A 14 -33.10 -136.63 REMARK 500 16 PRO A 28 39.62 -78.51 REMARK 500 16 TYR A 31 -154.01 -125.07 REMARK 500 16 LEU A 36 -67.18 -150.06 REMARK 500 16 CYS A 50 162.28 -47.44 REMARK 500 16 ALA A 57 63.23 -104.34 REMARK 500 16 LYS A 59 -170.90 69.37 REMARK 500 17 HIS A 8 -99.74 62.38 REMARK 500 17 ASP A 17 -154.64 -166.99 REMARK 500 17 TYR A 31 -152.23 -128.78 REMARK 500 17 HIS A 32 -157.03 -143.66 REMARK 500 17 LEU A 36 -157.81 -126.34 REMARK 500 18 SER A 5 -50.17 71.05 REMARK 500 18 VAL A 14 -73.16 -79.59 REMARK 500 18 TYR A 31 -159.06 -126.67 REMARK 500 18 PRO A 51 50.33 -66.48 REMARK 500 18 ARG A 52 -22.03 -166.21 REMARK 500 18 PRO A 56 109.30 -50.12 REMARK 500 19 HIS A 7 -124.89 -86.66 REMARK 500 19 HIS A 8 -100.87 69.46 REMARK 500 19 PHE A 11 -74.30 -124.15 REMARK 500 19 CYS A 12 138.39 159.35 REMARK 500 19 TYR A 31 -155.99 -126.01 REMARK 500 19 HIS A 32 -129.75 -128.67 REMARK 500 19 LEU A 58 -45.81 74.10 REMARK 500 19 LYS A 59 -66.79 69.65 REMARK 500 20 ASP A 6 -149.40 -167.88 REMARK 500 20 CYS A 12 -79.19 -62.86 REMARK 500 20 ARG A 13 -48.88 179.24 REMARK 500 20 THR A 26 -53.46 -122.45 REMARK 500 20 HIS A 32 -121.53 -126.77 REMARK 500 20 HIS A 34 8.32 -155.92 REMARK 500 20 CYS A 50 161.56 -49.62 REMARK 500 20 PRO A 51 39.42 -66.86 REMARK 500 20 ARG A 52 -39.02 -149.67 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 63 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 32 ND1 REMARK 620 2 CYS A 35 SG 110.1 REMARK 620 3 CYS A 15 SG 108.5 109.4 REMARK 620 4 CYS A 12 SG 109.0 111.3 108.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 62 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 CYS A 53 SG 109.4 REMARK 620 3 CYS A 27 SG 109.3 107.8 REMARK 620 4 CYS A 50 SG 111.8 109.6 108.8 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 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 REMARK 900 LOOP 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 ZN ZN A 63 ND1 HIS A 32 1555 1555 1.96 LINK ZN ZN A 62 SG CYS A 24 1555 1555 2.32 LINK ZN ZN A 62 SG CYS A 53 1555 1555 2.28 LINK ZN ZN A 62 SG CYS A 27 1555 1555 2.27 LINK ZN ZN A 62 SG CYS A 50 1555 1555 2.29 LINK ZN ZN A 63 SG CYS A 35 1555 1555 2.33 LINK ZN ZN A 63 SG CYS A 15 1555 1555 2.29 LINK ZN ZN A 63 SG CYS A 12 1555 1555 2.24
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