Header list of 1vd4.pdb file
Complete list - r 2 2 Bytes
HEADER TRANSCRIPTION 18-MAR-04 1VD4
TITLE SOLUTION STRUCTURE OF THE ZINC FINGER DOMAIN OF TFIIE ALPHA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRANSCRIPTION INITIATION FACTOR IIE, ALPHA SUBUNIT;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: ZINC FINGER DOMAIN;
COMPND 5 SYNONYM: TFIIE-ALPHA, GENERAL TRANSCRIPTION FACTOR IIE 56 KDA
COMPND 6 SUBUNIT, GENERAL TRANSCRIPTION FACTOR TFIIE ALPHA;
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: GTF2E1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11D
KEYWDS ZINC FINGER, TRANSCRIPTION
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR M.OKUDA,A.TANAKA,Y.ARAI,M.SATOH,H.OKAMURA,A.NAGADOI,F.HANAOKA,
AUTHOR 2 Y.OHKUMA,Y.NISHIMURA
REVDAT 3 02-MAR-22 1VD4 1 REMARK LINK
REVDAT 2 24-FEB-09 1VD4 1 VERSN
REVDAT 1 05-OCT-04 1VD4 0
JRNL AUTH M.OKUDA,A.TANAKA,Y.ARAI,M.SATOH,H.OKAMURA,A.NAGADOI,
JRNL AUTH 2 F.HANAOKA,Y.OHKUMA,Y.NISHIMURA
JRNL TITL A NOVEL ZINC FINGER STRUCTURE IN THE LARGE SUBUNIT OF HUMAN
JRNL TITL 2 GENERAL TRANSCRIPTION FACTOR TFIIE.
JRNL REF J.BIOL.CHEM. V. 279 51395 2004
JRNL REFN ISSN 0021-9258
JRNL PMID 15385556
JRNL DOI 10.1074/JBC.M404722200
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 2.6, X-PLOR 3.851
REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1VD4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAR-04.
REMARK 100 THE DEPOSITION ID IS D_1000006482.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 305
REMARK 210 PH : 6.0
REMARK 210 IONIC STRENGTH : 50MM NACL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 3-4MM TFIIE ALPHA ZINC FINGER
REMARK 210 DOMAIN, U-15N, U-15N, 13C; 20MM
REMARK 210 POTASSIUM PHOSPHATE BEFFER,
REMARK 210 0.03MM ZNCL2, 5MM D-DTT; 3-4MM
REMARK 210 TFIIE ALPHA ZINC FINGER DOMAIN,
REMARK 210 U-15N, U-15N, 13C; 20MM
REMARK 210 POTASSIUM PHOSPHATE BEFFER,
REMARK 210 0.03MM ZNCL2, 5MM D-DTT
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY; HNHA; HNCA-J;
REMARK 210 HNHB; HN(CO)HB; HNCG; HN(CO)CG;
REMARK 210 3D_13C-SEPARATED_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW 5, X-PLOR 3.851
REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED
REMARK 210 ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
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 : 20
REMARK 210
REMARK 210 REMARK: THE STRUCTURES WERE DETERMINED USING TRIPLE-RESONANCE NMR
REMARK 210 SPECTROSCOPY
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 O LEU A 144 H ARG A 153 1.56
REMARK 500 OD1 ASP A 138 H LEU A 139 1.59
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 118 -36.12 -163.20
REMARK 500 1 ARG A 119 -92.03 -138.92
REMARK 500 1 ASP A 120 -96.50 56.80
REMARK 500 1 THR A 122 -70.74 -110.33
REMARK 500 1 ASN A 123 -44.74 -161.46
REMARK 500 1 ARG A 124 -144.30 -128.30
REMARK 500 1 SER A 126 75.20 -160.77
REMARK 500 1 VAL A 131 -72.62 -96.21
REMARK 500 1 SER A 133 29.16 47.31
REMARK 500 1 SER A 134 -166.22 -76.67
REMARK 500 1 THR A 137 -165.57 -115.32
REMARK 500 1 CYS A 154 173.82 -45.50
REMARK 500 1 HIS A 158 30.50 33.61
REMARK 500 1 LYS A 170 -157.82 -101.18
REMARK 500 1 ALA A 173 109.68 63.07
REMARK 500 2 GLU A 115 63.93 64.38
REMARK 500 2 GLU A 118 -73.27 -63.36
REMARK 500 2 ASP A 120 -61.31 -171.55
REMARK 500 2 THR A 122 -70.53 -128.94
REMARK 500 2 ASN A 123 -52.74 -148.43
REMARK 500 2 SER A 126 110.60 -160.20
REMARK 500 2 VAL A 131 -73.72 -85.70
REMARK 500 2 SER A 134 -166.78 -79.25
REMARK 500 2 THR A 151 -156.71 -153.13
REMARK 500 2 CYS A 154 176.02 -46.58
REMARK 500 2 HIS A 158 31.83 30.63
REMARK 500 2 SER A 166 67.93 -165.91
REMARK 500 2 ALA A 167 51.17 -96.26
REMARK 500 2 PRO A 169 -88.64 -73.36
REMARK 500 2 LYS A 171 -69.54 -170.81
REMARK 500 2 ALA A 173 -89.99 51.16
REMARK 500 3 ASP A 117 23.35 -154.01
REMARK 500 3 GLU A 118 127.57 66.47
REMARK 500 3 ASP A 120 36.16 39.30
REMARK 500 3 ASN A 123 36.17 -89.67
REMARK 500 3 VAL A 131 -72.75 -95.04
REMARK 500 3 SER A 133 29.64 48.04
REMARK 500 3 CYS A 154 174.14 -46.82
REMARK 500 3 HIS A 158 33.53 30.34
REMARK 500 3 LYS A 170 155.52 67.11
REMARK 500 4 ARG A 119 -167.80 -108.99
REMARK 500 4 SER A 121 49.99 -144.91
REMARK 500 4 VAL A 131 -74.72 -84.37
REMARK 500 4 SER A 133 28.37 48.53
REMARK 500 4 CYS A 154 176.30 -47.49
REMARK 500 4 HIS A 158 28.70 37.38
REMARK 500 4 LYS A 170 38.55 -148.75
REMARK 500 4 ALA A 173 -175.58 -69.35
REMARK 500 5 THR A 116 -78.46 -119.18
REMARK 500 5 GLU A 118 -57.22 69.81
REMARK 500
REMARK 500 THIS ENTRY HAS 247 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 113 0.31 SIDE CHAIN
REMARK 500 1 ARG A 119 0.28 SIDE CHAIN
REMARK 500 1 ARG A 124 0.19 SIDE CHAIN
REMARK 500 1 ARG A 153 0.31 SIDE CHAIN
REMARK 500 1 ARG A 174 0.27 SIDE CHAIN
REMARK 500 2 ARG A 113 0.31 SIDE CHAIN
REMARK 500 2 ARG A 119 0.32 SIDE CHAIN
REMARK 500 2 ARG A 124 0.31 SIDE CHAIN
REMARK 500 2 ARG A 153 0.26 SIDE CHAIN
REMARK 500 2 ARG A 174 0.09 SIDE CHAIN
REMARK 500 3 ARG A 113 0.28 SIDE CHAIN
REMARK 500 3 ARG A 119 0.30 SIDE CHAIN
REMARK 500 3 ARG A 124 0.27 SIDE CHAIN
REMARK 500 3 ARG A 153 0.20 SIDE CHAIN
REMARK 500 3 ARG A 174 0.28 SIDE CHAIN
REMARK 500 4 ARG A 113 0.22 SIDE CHAIN
REMARK 500 4 ARG A 119 0.14 SIDE CHAIN
REMARK 500 4 ARG A 124 0.29 SIDE CHAIN
REMARK 500 4 ARG A 153 0.28 SIDE CHAIN
REMARK 500 4 ARG A 174 0.19 SIDE CHAIN
REMARK 500 5 ARG A 113 0.23 SIDE CHAIN
REMARK 500 5 ARG A 119 0.29 SIDE CHAIN
REMARK 500 5 ARG A 124 0.23 SIDE CHAIN
REMARK 500 5 ARG A 174 0.29 SIDE CHAIN
REMARK 500 6 ARG A 113 0.27 SIDE CHAIN
REMARK 500 6 ARG A 119 0.29 SIDE CHAIN
REMARK 500 6 ARG A 124 0.31 SIDE CHAIN
REMARK 500 6 ARG A 153 0.21 SIDE CHAIN
REMARK 500 6 ARG A 174 0.31 SIDE CHAIN
REMARK 500 7 ARG A 113 0.28 SIDE CHAIN
REMARK 500 7 ARG A 119 0.29 SIDE CHAIN
REMARK 500 7 ARG A 124 0.31 SIDE CHAIN
REMARK 500 7 ARG A 153 0.26 SIDE CHAIN
REMARK 500 7 ARG A 174 0.24 SIDE CHAIN
REMARK 500 8 ARG A 113 0.31 SIDE CHAIN
REMARK 500 8 ARG A 119 0.29 SIDE CHAIN
REMARK 500 8 ARG A 124 0.21 SIDE CHAIN
REMARK 500 8 ARG A 153 0.19 SIDE CHAIN
REMARK 500 8 ARG A 174 0.21 SIDE CHAIN
REMARK 500 9 ARG A 113 0.12 SIDE CHAIN
REMARK 500 9 ARG A 119 0.31 SIDE CHAIN
REMARK 500 9 ARG A 124 0.31 SIDE CHAIN
REMARK 500 9 ARG A 153 0.28 SIDE CHAIN
REMARK 500 9 ARG A 174 0.31 SIDE CHAIN
REMARK 500 10 ARG A 113 0.31 SIDE CHAIN
REMARK 500 10 ARG A 119 0.15 SIDE CHAIN
REMARK 500 10 ARG A 124 0.09 SIDE CHAIN
REMARK 500 10 ARG A 153 0.20 SIDE CHAIN
REMARK 500 10 ARG A 174 0.31 SIDE CHAIN
REMARK 500 11 ARG A 113 0.31 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 97 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 175 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 129 SG
REMARK 620 2 CYS A 132 SG 90.3
REMARK 620 3 CYS A 154 SG 113.8 101.7
REMARK 620 4 CYS A 157 SG 109.1 100.6 131.0
REMARK 620 N 1 2 3
REMARK 650
REMARK 650 HELIX
REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED
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 175
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1D8J RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BATA (20
REMARK 900 STRUCTURES)
REMARK 900 RELATED ID: 1D8K RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BATA
REMARK 900 (AVERAGE STRUCTURE)
DBREF 1VD4 A 113 174 UNP P29083 T2EA_HUMAN 113 174
SEQRES 1 A 62 ARG ILE GLU THR ASP GLU ARG ASP SER THR ASN ARG ALA
SEQRES 2 A 62 SER PHE LYS CYS PRO VAL CYS SER SER THR PHE THR ASP
SEQRES 3 A 62 LEU GLU ALA ASN GLN LEU PHE ASP PRO MET THR GLY THR
SEQRES 4 A 62 PHE ARG CYS THR PHE CYS HIS THR GLU VAL GLU GLU ASP
SEQRES 5 A 62 GLU SER ALA MET PRO LYS LYS ASP ALA ARG
HET ZN A 175 1
HETNAM ZN ZINC ION
FORMUL 2 ZN ZN 2+
HELIX 1 1 ASP A 138 LEU A 144 1 7
SHEET 1 A 3 GLU A 162 ASP A 164 0
SHEET 2 A 3 SER A 126 CYS A 129 -1 O SER A 126 N ASP A 164
SHEET 3 A 3 SER A 134 PHE A 136 -1 O SER A 134 N CYS A 129
SHEET 1 B 3 PHE A 145 ASP A 146 0
SHEET 2 B 3 THR A 151 CYS A 154 -1 O THR A 151 N ASP A 146
SHEET 3 B 3 THR A 159 VAL A 161 -1 O THR A 159 N CYS A 154
LINK SG CYS A 129 ZN ZN A 175 1555 1555 2.46
LINK SG CYS A 132 ZN ZN A 175 1555 1555 2.79
LINK SG CYS A 154 ZN ZN A 175 1555 1555 2.02
LINK SG CYS A 157 ZN ZN A 175 1555 1555 2.11
SITE 1 AC1 5 CYS A 129 CYS A 132 CYS A 154 CYS A 157
SITE 2 AC1 5 THR A 159
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
Complete list - r 2 2 Bytes