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
(ATOM LINES ARE NOT SHOWN.)
END