Header list of 1y5o.pdb file
Complete list - t 20 2 Bytes
HEADER TRANSCRIPTION 02-DEC-04 1Y5O
TITLE NMR STRUCTURE OF THE AMINO-TERMINAL DOMAIN FROM THE TFB1 SUBUNIT OF
TITLE 2 YEAST TFIIH
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RNA POLYMERASE II TRANSCRIPTION FACTOR B 73 KDA SUBUNIT;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 1-115;
COMPND 5 SYNONYM: TFB1;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: 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 GENE: TFB1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TOPP2;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-2T
KEYWDS TFIIH, TFB1, PH DOMAIN, PHOSPHOINOSITIDES, VP16, TRANSCRIPTION
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR P.DI LELLO,B.D.NGUYEN,T.N.JONES,K.POTEMPA,M.S.KOBOR,P.LEGAULT,
AUTHOR 2 J.G.OMICHINSKI
REVDAT 4 20-OCT-21 1Y5O 1 REMARK SEQADV
REVDAT 3 24-FEB-09 1Y5O 1 VERSN
REVDAT 2 31-MAY-05 1Y5O 1 JRNL
REVDAT 1 17-MAY-05 1Y5O 0
JRNL AUTH P.DI LELLO,B.D.NGUYEN,T.N.JONES,K.POTEMPA,M.S.KOBOR,
JRNL AUTH 2 P.LEGAULT,J.G.OMICHINSKI
JRNL TITL NMR STRUCTURE OF THE AMINO-TERMINAL DOMAIN FROM THE TFB1
JRNL TITL 2 SUBUNIT OF TFIIH AND CHARACTERIZATION OF ITS
JRNL TITL 3 PHOSPHOINOSITIDE AND VP16 BINDING SITES
JRNL REF BIOCHEMISTRY V. 44 7678 2005
JRNL REFN ISSN 0006-2960
JRNL PMID 15909982
JRNL DOI 10.1021/BI050099S
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.0
REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-
REMARK 3 KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ,
REMARK 3 RICE, SIMONSON, WARREN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE THREE-DIMENSIONAL STRUCTURES OF THE
REMARK 3 AMINO-TERMINAL DOMAIN OF TFB1 WERE DETERMINED USING A SET OF
REMARK 3 1208 NOE-DERIVED DISTANCE RESTRAINTS, 124 BACKBONE DIHEDRAL
REMARK 3 ANGLE (PHI AND PSI) RESTRAINTS AND 20 DISTANCE RESTRAINTS FROM
REMARK 3 HYDROGEN BONDS.
REMARK 4
REMARK 4 1Y5O COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-DEC-04.
REMARK 100 THE DEPOSITION ID IS D_1000031147.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 300
REMARK 210 PH : 6.5
REMARK 210 IONIC STRENGTH : 20 MM SODIUM PHOSPHATE
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.2 MM TFB1 [UNLABELED], 20 MM
REMARK 210 PHOSPHATE BUFFER, 1MM EDTA, 100%
REMARK 210 D2O; 1.2 MM TFB1 [U-15N], 20 MM
REMARK 210 PHOSPHATE BUFFER, 1MM EDTA, 90%
REMARK 210 H2O, 10% D2O; 1.2 MM TFB1 [U-15N,
REMARK 210 13C], 20 MM PHOSPHATE BUFFER,
REMARK 210 1MM EDTA, 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D 15N-EDITED NOESY
REMARK 210 -HSQC; 2D 1H-15N HSQC; 3D 13C-
REMARK 210 EDITED HMQC-NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : UNITY
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR 6.1.C 6.1.C, NMRPIPE 2.2,
REMARK 210 NMRVIEW 5.0.4, CNS 1.0
REMARK 210 METHOD USED : SIMULATED ANNEALING, WITH A
REMARK 210 COMBINATION OF TORSION ANGLE
REMARK 210 DYNAMICS AND CARTESIAN DYNAMICS.
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 62
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED MODELS ARE THE 20
REMARK 210 STRUCTURES WITH NO UPPER BOUND
REMARK 210 VIOLATION GREATER THAN 0.2
REMARK 210 ARMSTRONG, NO DIHEDRAL ANGLE
REMARK 210 RESTRAINT VIOLATION GREATER THAN
REMARK 210 2 DEGREES AND WITH THE LOWEST
REMARK 210 ENERGIES.
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: LOWEST ENERGY
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
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 10 49.97 78.08
REMARK 500 1 SER A 23 113.41 -165.82
REMARK 500 1 ALA A 25 172.04 -54.32
REMARK 500 1 LYS A 65 -176.44 50.09
REMARK 500 1 VAL A 66 -67.87 -107.87
REMARK 500 1 GLU A 68 38.90 -147.82
REMARK 500 1 VAL A 81 108.83 -55.69
REMARK 500 2 SER A 2 -45.15 -159.98
REMARK 500 2 GLU A 10 49.77 78.01
REMARK 500 2 ALA A 25 172.05 -54.33
REMARK 500 2 ILE A 45 97.99 -66.43
REMARK 500 2 GLU A 68 43.87 -155.57
REMARK 500 2 LYS A 83 -61.23 179.86
REMARK 500 3 SER A 4 121.50 -179.90
REMARK 500 3 GLU A 10 49.91 77.89
REMARK 500 3 SER A 23 113.38 -166.50
REMARK 500 3 PRO A 84 93.24 -68.44
REMARK 500 4 SER A 4 170.31 58.14
REMARK 500 4 GLU A 10 49.91 78.18
REMARK 500 4 SER A 23 112.86 -165.48
REMARK 500 4 ALA A 25 170.15 -54.26
REMARK 500 4 ILE A 45 94.56 -64.81
REMARK 500 4 LYS A 65 166.44 55.30
REMARK 500 4 LYS A 71 104.86 57.98
REMARK 500 4 ARG A 72 129.04 62.81
REMARK 500 4 LYS A 83 -54.57 179.38
REMARK 500 5 SER A 2 167.04 59.01
REMARK 500 5 HIS A 3 128.81 62.90
REMARK 500 5 SER A 4 127.37 62.98
REMARK 500 5 GLU A 10 49.85 78.04
REMARK 500 5 SER A 23 113.11 -166.77
REMARK 500 5 ILE A 45 94.03 -62.39
REMARK 500 5 VAL A 66 -67.47 -127.15
REMARK 500 5 GLU A 76 39.08 -96.16
REMARK 500 5 VAL A 80 44.77 -178.26
REMARK 500 6 SER A 2 -45.05 -160.93
REMARK 500 6 SER A 4 172.12 57.65
REMARK 500 6 GLU A 10 49.66 77.87
REMARK 500 6 ALA A 25 172.18 -54.46
REMARK 500 6 ILE A 45 93.61 -59.84
REMARK 500 6 LYS A 71 102.99 59.56
REMARK 500 6 GLU A 76 32.50 -98.93
REMARK 500 6 ASN A 78 -171.46 45.99
REMARK 500 7 SER A 4 118.29 -179.14
REMARK 500 7 GLU A 10 49.70 77.96
REMARK 500 7 SER A 23 113.14 -166.20
REMARK 500 7 ALA A 25 170.48 -54.39
REMARK 500 7 ILE A 45 92.09 -58.76
REMARK 500 7 GLU A 68 38.92 -141.45
REMARK 500 7 GLU A 76 38.22 -95.69
REMARK 500
REMARK 500 THIS ENTRY HAS 144 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6225 RELATED DB: BMRB
REMARK 900 1H, 15N, AND 13C RESONANCE ASSIGNMENT OF THE AMINO-TERMINAL DOMAIN
REMARK 900 OF TFB1 SUBUNIT OF YEAST TFIIH
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE FRAGMENT OF TFB1 STUDIED IN THIS CASE CONTAINS TWO
REMARK 999 EXTRA RESIDUES (GLY SER) AT THE N-TERMINUS AND FOUR
REMARK 999 EXTRA RESIDUES (GLY ASN SER SER) AT THE C-TERMINUS
REMARK 999 AS A CONSEQUENCE OF CLONING ARTIFACTS. THESE EXTRA
REMARK 999 AMINO ACIDS WERE NOT INCLUDED IN THE STRUCTURE
REMARK 999 CALCULATIONS AND THEREFORE THEY ARE NOT PRESENT IN
REMARK 999 DEPOSITED STRUCTURES
DBREF 1Y5O A 1 115 UNP P32776 TFB1_YEAST 1 115
SEQADV 1Y5O PRO A 1 UNP P32776 MET 1 ENGINEERED MUTATION
SEQRES 1 A 115 PRO SER HIS SER GLY ALA ALA ILE PHE GLU LYS VAL SER
SEQRES 2 A 115 GLY ILE ILE ALA ILE ASN GLU ASP VAL SER PRO ALA GLU
SEQRES 3 A 115 LEU THR TRP ARG SER THR ASP GLY ASP LYS VAL HIS THR
SEQRES 4 A 115 VAL VAL LEU SER THR ILE ASP LYS LEU GLN ALA THR PRO
SEQRES 5 A 115 ALA SER SER GLU LYS MET MET LEU ARG LEU ILE GLY LYS
SEQRES 6 A 115 VAL ASP GLU SER LYS LYS ARG LYS ASP ASN GLU GLY ASN
SEQRES 7 A 115 GLU VAL VAL PRO LYS PRO GLN ARG HIS MET PHE SER PHE
SEQRES 8 A 115 ASN ASN ARG THR VAL MET ASP ASN ILE LYS MET THR LEU
SEQRES 9 A 115 GLN GLN ILE ILE SER ARG TYR LYS ASP ALA ASP
HELIX 1 1 ASN A 93 ASP A 115 1 23
SHEET 1 A 4 SER A 4 ILE A 8 0
SHEET 2 A 4 SER A 13 ASN A 19 -1 O ILE A 16 N GLY A 5
SHEET 3 A 4 GLU A 26 SER A 31 -1 O GLU A 26 N ASN A 19
SHEET 4 A 4 VAL A 37 VAL A 41 -1 O HIS A 38 N TRP A 29
SHEET 1 B 3 GLN A 49 ALA A 50 0
SHEET 2 B 3 MET A 58 GLY A 64 -1 O ARG A 61 N GLN A 49
SHEET 3 B 3 GLN A 85 PHE A 91 -1 O PHE A 91 N MET A 58
CISPEP 1 SER A 23 PRO A 24 1 0.08
CISPEP 2 SER A 23 PRO A 24 2 0.23
CISPEP 3 SER A 23 PRO A 24 3 0.07
CISPEP 4 SER A 23 PRO A 24 4 0.02
CISPEP 5 SER A 23 PRO A 24 5 -0.01
CISPEP 6 SER A 23 PRO A 24 6 0.18
CISPEP 7 SER A 23 PRO A 24 7 0.05
CISPEP 8 SER A 23 PRO A 24 8 0.11
CISPEP 9 SER A 23 PRO A 24 9 0.08
CISPEP 10 SER A 23 PRO A 24 10 0.13
CISPEP 11 SER A 23 PRO A 24 11 -0.01
CISPEP 12 SER A 23 PRO A 24 12 -0.04
CISPEP 13 SER A 23 PRO A 24 13 0.09
CISPEP 14 SER A 23 PRO A 24 14 -0.04
CISPEP 15 SER A 23 PRO A 24 15 -0.01
CISPEP 16 SER A 23 PRO A 24 16 0.11
CISPEP 17 SER A 23 PRO A 24 17 0.09
CISPEP 18 SER A 23 PRO A 24 18 0.09
CISPEP 19 SER A 23 PRO A 24 19 0.18
CISPEP 20 SER A 23 PRO A 24 20 0.04
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 - t 20 2 Bytes