HEADER ZINC FINGER DNA BINDING DOMAIN 04-APR-96 1ZFD
TITLE SWI5 ZINC FINGER DOMAIN 2, NMR, 45 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: SWI5;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: ZINC FINGER DOMAIN 2;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;
SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST;
SOURCE 4 ORGANISM_TAXID: 4932;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PRK172;
SOURCE 8 OTHER_DETAILS: T7 PROMOTER
KEYWDS DNA BINDING MOTIF, ZINC FINGER DNA BINDING DOMAIN
EXPDTA SOLUTION NMR
NUMMDL 45
AUTHOR D.NEUHAUS,Y.NAKASEKO,J.W.R.SCHWABE,D.RHODES,A.KLUG
REVDAT 3 02-MAR-22 1ZFD 1 REMARK LINK
REVDAT 2 24-FEB-09 1ZFD 1 VERSN
REVDAT 1 14-OCT-96 1ZFD 0
JRNL AUTH D.NEUHAUS,Y.NAKASEKO,J.W.SCHWABE,A.KLUG
JRNL TITL SOLUTION STRUCTURES OF TWO ZINC-FINGER DOMAINS FROM SWI5
JRNL TITL 2 OBTAINED USING TWO-DIMENSIONAL 1H NUCLEAR MAGNETIC RESONANCE
JRNL TITL 3 SPECTROSCOPY. A ZINC-FINGER STRUCTURE WITH A THIRD STRAND OF
JRNL TITL 4 BETA-SHEET.
JRNL REF J.MOL.BIOL. V. 228 637 1992
JRNL REFN ISSN 0022-2836
JRNL PMID 1453468
JRNL DOI 10.1016/0022-2836(92)90846-C
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH Y.NAKASEKO,D.NEUHAUS,A.KLUG,D.RHODES
REMARK 1 TITL ADJACENT ZINC-FINGER MOTIFS IN MULTIPLE ZINC-FINGER PEPTIDES
REMARK 1 TITL 2 FROM SWI5 FORM STRUCTURALLY INDEPENDENT, FLEXIBLY LINKED
REMARK 1 TITL 3 DOMAINS
REMARK 1 REF J.MOL.BIOL. V. 228 619 1992
REMARK 1 REFN ISSN 0022-2836
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 2.1
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1ZFD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000177472.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : NULL
REMARK 210 SPECTROMETER MODEL : NULL
REMARK 210 SPECTROMETER MANUFACTURER : NULL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : NULL
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 45
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
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: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 1 HIS A 46 CG HIS A 46 ND1 -0.120
REMARK 500 1 HIS A 57 CG HIS A 57 ND1 -0.120
REMARK 500 1 HIS A 62 CG HIS A 62 ND1 -0.120
REMARK 500 1 HIS A 66 CG HIS A 66 ND1 -0.121
REMARK 500 2 HIS A 46 CG HIS A 46 ND1 -0.120
REMARK 500 2 HIS A 57 CG HIS A 57 ND1 -0.120
REMARK 500 2 HIS A 62 CG HIS A 62 ND1 -0.122
REMARK 500 2 HIS A 66 CG HIS A 66 ND1 -0.124
REMARK 500 3 HIS A 46 CG HIS A 46 ND1 -0.121
REMARK 500 3 HIS A 57 CG HIS A 57 ND1 -0.120
REMARK 500 3 HIS A 62 CG HIS A 62 ND1 -0.121
REMARK 500 3 HIS A 66 CG HIS A 66 ND1 -0.122
REMARK 500 4 HIS A 46 CG HIS A 46 ND1 -0.120
REMARK 500 4 HIS A 57 CG HIS A 57 ND1 -0.120
REMARK 500 4 HIS A 62 CG HIS A 62 ND1 -0.122
REMARK 500 4 HIS A 66 CG HIS A 66 ND1 -0.121
REMARK 500 5 HIS A 46 CG HIS A 46 ND1 -0.120
REMARK 500 5 HIS A 57 CG HIS A 57 ND1 -0.121
REMARK 500 5 HIS A 62 CG HIS A 62 ND1 -0.121
REMARK 500 5 HIS A 66 CG HIS A 66 ND1 -0.122
REMARK 500 6 HIS A 46 CG HIS A 46 ND1 -0.119
REMARK 500 6 HIS A 57 CG HIS A 57 ND1 -0.119
REMARK 500 6 HIS A 62 CG HIS A 62 ND1 -0.122
REMARK 500 6 HIS A 66 CG HIS A 66 ND1 -0.123
REMARK 500 7 HIS A 46 CG HIS A 46 ND1 -0.120
REMARK 500 7 HIS A 57 CG HIS A 57 ND1 -0.120
REMARK 500 7 HIS A 62 CG HIS A 62 ND1 -0.122
REMARK 500 7 HIS A 66 CG HIS A 66 ND1 -0.122
REMARK 500 8 HIS A 46 CG HIS A 46 ND1 -0.119
REMARK 500 8 HIS A 57 CG HIS A 57 ND1 -0.122
REMARK 500 8 HIS A 62 CG HIS A 62 ND1 -0.122
REMARK 500 8 HIS A 66 CG HIS A 66 ND1 -0.121
REMARK 500 9 HIS A 46 CG HIS A 46 ND1 -0.120
REMARK 500 9 HIS A 57 CG HIS A 57 ND1 -0.120
REMARK 500 9 HIS A 62 CG HIS A 62 ND1 -0.119
REMARK 500 9 HIS A 66 CG HIS A 66 ND1 -0.122
REMARK 500 10 HIS A 46 CG HIS A 46 ND1 -0.122
REMARK 500 10 HIS A 57 CG HIS A 57 ND1 -0.121
REMARK 500 10 HIS A 62 CG HIS A 62 ND1 -0.121
REMARK 500 10 HIS A 66 CG HIS A 66 ND1 -0.121
REMARK 500 11 HIS A 46 CG HIS A 46 ND1 -0.120
REMARK 500 11 HIS A 57 CG HIS A 57 ND1 -0.121
REMARK 500 11 HIS A 62 CG HIS A 62 ND1 -0.120
REMARK 500 11 HIS A 66 CG HIS A 66 ND1 -0.123
REMARK 500 12 HIS A 46 CG HIS A 46 ND1 -0.120
REMARK 500 12 HIS A 57 CG HIS A 57 ND1 -0.119
REMARK 500 12 HIS A 62 CG HIS A 62 ND1 -0.120
REMARK 500 12 HIS A 66 CG HIS A 66 ND1 -0.122
REMARK 500 13 HIS A 46 CG HIS A 46 ND1 -0.123
REMARK 500 13 HIS A 57 CG HIS A 57 ND1 -0.121
REMARK 500
REMARK 500 THIS ENTRY HAS 180 BOND DEVIATIONS.
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 SER A 43 76.35 -110.45
REMARK 500 1 ASP A 50 40.35 -170.03
REMARK 500 1 ASN A 56 -62.04 -94.08
REMARK 500 1 HIS A 66 -5.14 -59.56
REMARK 500 1 GLN A 67 -70.36 -91.14
REMARK 500 1 GLU A 68 156.78 55.31
REMARK 500 2 CYS A 44 158.37 -44.36
REMARK 500 2 PRO A 47 96.95 -47.60
REMARK 500 2 ASP A 50 23.18 -162.22
REMARK 500 3 TYR A 42 70.74 -100.85
REMARK 500 3 ASP A 45 55.12 -141.09
REMARK 500 3 ASP A 50 65.18 -163.19
REMARK 500 3 GLN A 67 -19.19 -42.47
REMARK 500 3 LYS A 69 34.17 -79.12
REMARK 500 4 SER A 43 79.09 -105.84
REMARK 500 4 CYS A 44 158.99 -47.99
REMARK 500 4 ASP A 45 48.05 -154.96
REMARK 500 4 PRO A 47 103.50 -48.37
REMARK 500 4 ASP A 50 19.35 -162.81
REMARK 500 4 VAL A 54 -35.28 -134.65
REMARK 500 4 ARG A 55 -145.52 -76.06
REMARK 500 4 ASN A 56 -71.88 -133.45
REMARK 500 4 HIS A 57 -19.20 -46.64
REMARK 500 4 GLN A 67 84.98 -164.32
REMARK 500 4 GLU A 68 64.63 -106.12
REMARK 500 4 LYS A 69 87.60 51.42
REMARK 500 5 SER A 43 79.19 -111.37
REMARK 500 5 CYS A 44 153.90 -44.52
REMARK 500 5 ASP A 50 19.78 -160.15
REMARK 500 5 ASN A 56 -67.09 -95.62
REMARK 500 5 HIS A 66 25.05 -77.88
REMARK 500 5 LYS A 69 -151.30 -63.26
REMARK 500 6 ARG A 40 71.03 46.74
REMARK 500 6 PRO A 47 99.34 -47.16
REMARK 500 6 ASP A 50 20.28 -164.60
REMARK 500 6 VAL A 54 -36.96 -134.79
REMARK 500 6 ASN A 56 -62.62 -98.45
REMARK 500 6 HIS A 66 -3.30 -57.30
REMARK 500 6 GLU A 68 99.89 49.93
REMARK 500 7 PRO A 41 -86.92 -69.80
REMARK 500 7 TYR A 42 66.05 2.21
REMARK 500 7 CYS A 44 153.07 -45.17
REMARK 500 7 PRO A 47 101.11 -45.88
REMARK 500 7 ASP A 50 21.99 -162.58
REMARK 500 7 LYS A 64 -11.33 -49.60
REMARK 500 7 GLN A 67 -92.13 -64.96
REMARK 500 8 TYR A 42 73.46 -106.77
REMARK 500 8 ASP A 50 57.06 -173.70
REMARK 500 8 VAL A 54 -39.24 -162.04
REMARK 500 8 ASN A 56 -177.08 -54.96
REMARK 500
REMARK 500 THIS ENTRY HAS 353 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 ARG A 40 0.32 SIDE CHAIN
REMARK 500 1 ARG A 55 0.32 SIDE CHAIN
REMARK 500 2 ARG A 40 0.21 SIDE CHAIN
REMARK 500 2 ARG A 55 0.28 SIDE CHAIN
REMARK 500 3 ARG A 40 0.19 SIDE CHAIN
REMARK 500 3 ARG A 55 0.28 SIDE CHAIN
REMARK 500 3 ARG A 61 0.08 SIDE CHAIN
REMARK 500 4 ARG A 40 0.29 SIDE CHAIN
REMARK 500 4 ARG A 55 0.20 SIDE CHAIN
REMARK 500 4 ARG A 61 0.29 SIDE CHAIN
REMARK 500 5 ARG A 40 0.30 SIDE CHAIN
REMARK 500 5 ARG A 55 0.28 SIDE CHAIN
REMARK 500 5 ARG A 61 0.10 SIDE CHAIN
REMARK 500 6 ARG A 40 0.16 SIDE CHAIN
REMARK 500 6 ARG A 55 0.28 SIDE CHAIN
REMARK 500 6 ARG A 61 0.17 SIDE CHAIN
REMARK 500 7 ARG A 40 0.31 SIDE CHAIN
REMARK 500 7 ARG A 61 0.20 SIDE CHAIN
REMARK 500 8 ARG A 40 0.12 SIDE CHAIN
REMARK 500 8 ARG A 55 0.23 SIDE CHAIN
REMARK 500 8 ARG A 61 0.20 SIDE CHAIN
REMARK 500 9 ARG A 40 0.26 SIDE CHAIN
REMARK 500 9 ARG A 55 0.24 SIDE CHAIN
REMARK 500 10 ARG A 55 0.27 SIDE CHAIN
REMARK 500 10 ARG A 61 0.28 SIDE CHAIN
REMARK 500 11 ARG A 40 0.22 SIDE CHAIN
REMARK 500 11 ARG A 55 0.21 SIDE CHAIN
REMARK 500 12 ARG A 40 0.18 SIDE CHAIN
REMARK 500 12 ARG A 61 0.31 SIDE CHAIN
REMARK 500 13 ARG A 40 0.29 SIDE CHAIN
REMARK 500 13 ARG A 55 0.13 SIDE CHAIN
REMARK 500 13 ARG A 61 0.32 SIDE CHAIN
REMARK 500 14 ARG A 40 0.12 SIDE CHAIN
REMARK 500 14 ARG A 55 0.32 SIDE CHAIN
REMARK 500 14 ARG A 61 0.31 SIDE CHAIN
REMARK 500 15 ARG A 40 0.31 SIDE CHAIN
REMARK 500 15 ARG A 55 0.26 SIDE CHAIN
REMARK 500 15 ARG A 61 0.32 SIDE CHAIN
REMARK 500 16 ARG A 40 0.19 SIDE CHAIN
REMARK 500 16 ARG A 55 0.29 SIDE CHAIN
REMARK 500 17 ARG A 40 0.29 SIDE CHAIN
REMARK 500 17 ARG A 55 0.32 SIDE CHAIN
REMARK 500 18 ARG A 40 0.26 SIDE CHAIN
REMARK 500 18 ARG A 55 0.20 SIDE CHAIN
REMARK 500 18 ARG A 61 0.28 SIDE CHAIN
REMARK 500 19 ARG A 40 0.19 SIDE CHAIN
REMARK 500 19 ARG A 61 0.12 SIDE CHAIN
REMARK 500 20 ARG A 40 0.17 SIDE CHAIN
REMARK 500 20 ARG A 55 0.32 SIDE CHAIN
REMARK 500 20 ARG A 61 0.25 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 120 PLANE DEVIATIONS.
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 71 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 44 SG
REMARK 620 2 CYS A 49 SG 110.0
REMARK 620 3 HIS A 62 NE2 111.9 110.9
REMARK 620 4 HIS A 66 NE2 108.9 112.3 102.6
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 71
DBREF 1ZFD A 39 70 UNP P08153 SWI5_YEAST 577 608
SEQRES 1 A 32 ASP ARG PRO TYR SER CYS ASP HIS PRO GLY CYS ASP LYS
SEQRES 2 A 32 ALA PHE VAL ARG ASN HIS ASP LEU ILE ARG HIS LYS LYS
SEQRES 3 A 32 SER HIS GLN GLU LYS ALA
HET ZN A 71 1
HETNAM ZN ZINC ION
FORMUL 2 ZN ZN 2+
HELIX 1 1 ASN A 56 HIS A 66 1IRREGULAR R/H ALPHA 11
SHEET 1 1 2 TYR A 42 CYS A 44 0
SHEET 2 1 2 LYS A 51 PHE A 53 -1 N PHE A 53 O TYR A 42
LINK SG CYS A 44 ZN ZN A 71 1555 1555 2.29
LINK SG CYS A 49 ZN ZN A 71 1555 1555 2.30
LINK NE2 HIS A 62 ZN ZN A 71 1555 1555 1.99
LINK NE2 HIS A 66 ZN ZN A 71 1555 1555 2.00
SITE 1 AC1 4 CYS A 44 CYS A 49 HIS A 62 HIS A 66
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
