Header list of 1i11.pdb file
Complete list - t 27 2 Bytes
HEADER DNA BINDING PROTEIN 30-JAN-01 1I11
TITLE SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN, SOX-5 HMG BOX FROM MOUSE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRANSCRIPTION FACTOR SOX-5;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: HMG BOX;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE;
SOURCE 4 ORGANISM_TAXID: 10090;
SOURCE 5 ORGAN: TESTIS;
SOURCE 6 GENE: SOX-5;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) PLYSS;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGEX-2T
KEYWDS HMG BOX, DNA BENDING, DNA RECOGNITION, CHROMATIN, DNA BINDING
KEYWDS 2 PROTEIN, DNA SEQUENCE SPECIFIC, TESTIS DETERMINING.
EXPDTA SOLUTION NMR
NUMMDL 30
AUTHOR P.D.CARY,C.M.READ,B.DAVIS,P.C.DRISCOLL,C.CRANE-ROBINSON
REVDAT 3 27-OCT-21 1I11 1 REMARK
REVDAT 2 24-FEB-09 1I11 1 VERSN
REVDAT 1 14-FEB-01 1I11 0
JRNL AUTH P.D.CARY,C.M.READ,B.DAVIS,P.C.DRISCOLL,C.CRANE-ROBINSON
JRNL TITL SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF THE DNA-BINDING
JRNL TITL 2 DOMAIN OF MOUSE SOX-5.
JRNL REF PROTEIN SCI. V. 10 83 2001
JRNL REFN ISSN 0961-8368
JRNL PMID 11266597
JRNL DOI 10.1110/PS.32801
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.851
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON A TOTAL OF 1383
REMARK 3 NONREDUNDANT DISTANCE NOE RESTRAINTS, 61 DIHEDRAL ANGLE
REMARK 3 RESTRAINTS AND 24 PAIRED DISTANCE RESTRAINTS FOR HYDROGEN BONDS.
REMARK 4
REMARK 4 1I11 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-01.
REMARK 100 THE DEPOSITION ID IS D_1000012772.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298.00
REMARK 210 PH : 6.20
REMARK 210 IONIC STRENGTH : 75 MM KPO4
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 2-3 MM [U-100% 15N] SOX-5 HMG
REMARK 210 BOX, 75 MM POTASSIUM PHOSPHATE
REMARK 210 BUFFER, 0.5 MM DTT, 90% H2O/10%
REMARK 210 D2O; 3 MM SOX-5 HMG BOX, 75 MM
REMARK 210 POTASSIUM PHOSPHATE BUFFER, 0.5
REMARK 210 MM DTT, 100% D2O; 1 MM [U-100%
REMARK 210 15N] SOX-5 HMG BOX, 75 MM
REMARK 210 POTASSIUM PHOSPHATE BUFFER, 0.5
REMARK 210 MM DTT, 90% H2O/10% D2O; 3 MM
REMARK 210 SOX-5 HMG BOX, 75 MM POTASSIUM
REMARK 210 PHOSPHATE BUFFER, 0.5 MM DTT, 90%
REMARK 210 H2O/10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D_1H_NOESY; 2D_15N-1H_HMQC-J;
REMARK 210 3D_15N-1H_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : OMEGA; AM; UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : GE; BRUKER; VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 2.30, NMRVIEW 3, INSIGHT
REMARK 210 II 97.0
REMARK 210 METHOD USED : SIMULATING ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES
REMARK 210 WITH THE LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING A COMBINATION OF 2D
REMARK 210 AND 3D NMR SPECTRA. THE 30 STRUCTURES ARE ALIGNED OVER ALL
REMARK 210 BACKBONE ATOMS FOR RESIDUES 10-25 AND 32-43. MODEL 1 IS THE
REMARK 210 MINIMUM ENERGY AND REFERENCE STRUCTURE FOR THE OTHER 29
REMARK 210 STRUCTURES.
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 MODELS 1-30
REMARK 465 RES C SSSEQI
REMARK 465 GLY A -1
REMARK 465 SER A 0
REMARK 465 LYS A 71
REMARK 465 TYR A 72
REMARK 465 LYS A 73
REMARK 465 PRO A 74
REMARK 465 ARG A 75
REMARK 465 PRO A 76
REMARK 465 LYS A 77
REMARK 465 ARG A 78
REMARK 465 THR A 79
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 PHE A 10 H ALA A 14 1.45
REMARK 500 OD1 ASN A 8 H PHE A 10 1.46
REMARK 500 O ARG A 18 H LEU A 22 1.48
REMARK 500 O ALA A 9 H TRP A 13 1.51
REMARK 500 O LEU A 37 H TRP A 41 1.59
REMARK 500 O ASP A 16 H LYS A 20 1.60
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 HIS A 2 54.68 -117.77
REMARK 500 1 MET A 7 -166.94 -107.47
REMARK 500 1 ASN A 8 -179.38 177.75
REMARK 500 1 MET A 28 90.09 -62.47
REMARK 500 1 MET A 44 -133.77 -86.76
REMARK 500 1 ASN A 46 -59.22 70.89
REMARK 500 2 HIS A 2 55.36 -177.47
REMARK 500 2 LYS A 4 87.73 -69.75
REMARK 500 2 MET A 28 91.99 -64.07
REMARK 500 2 HIS A 29 -162.76 -77.85
REMARK 500 2 MET A 44 -153.07 -82.09
REMARK 500 2 ASN A 46 -56.29 79.15
REMARK 500 3 PHE A 25 73.07 -153.79
REMARK 500 3 MET A 28 91.64 -62.76
REMARK 500 3 HIS A 29 -158.43 -77.77
REMARK 500 3 SER A 31 -26.36 -40.00
REMARK 500 3 MET A 44 -134.59 -87.33
REMARK 500 3 THR A 45 20.60 -148.43
REMARK 500 3 ASN A 46 -57.19 67.94
REMARK 500 3 PRO A 68 -72.19 -79.61
REMARK 500 4 HIS A 2 62.62 -165.54
REMARK 500 4 MET A 7 -168.45 -106.25
REMARK 500 4 ASN A 8 -176.07 176.49
REMARK 500 4 MET A 28 91.00 -63.53
REMARK 500 4 SER A 31 -28.31 -37.38
REMARK 500 4 MET A 44 -147.12 -90.59
REMARK 500 4 THR A 45 -86.14 -151.04
REMARK 500 4 ASN A 46 -43.72 -162.35
REMARK 500 4 PRO A 68 -87.50 -78.13
REMARK 500 4 ASP A 69 56.17 -92.10
REMARK 500 5 HIS A 2 74.70 -119.74
REMARK 500 5 ASN A 8 178.45 179.89
REMARK 500 5 PHE A 25 74.54 -155.60
REMARK 500 5 MET A 28 92.27 -63.43
REMARK 500 5 HIS A 29 -163.93 -79.88
REMARK 500 5 SER A 31 -27.94 -38.38
REMARK 500 5 ASN A 46 -46.78 -19.63
REMARK 500 5 TYR A 67 73.85 -154.71
REMARK 500 6 HIS A 2 48.76 -168.68
REMARK 500 6 ILE A 3 52.77 -111.16
REMARK 500 6 LYS A 4 87.01 -69.29
REMARK 500 6 PRO A 6 49.08 -79.41
REMARK 500 6 MET A 7 -161.10 -109.14
REMARK 500 6 ASN A 8 178.16 178.62
REMARK 500 6 PHE A 25 72.85 -156.27
REMARK 500 6 MET A 28 93.01 -62.53
REMARK 500 6 HIS A 29 -161.42 -78.23
REMARK 500 6 ASN A 30 -73.25 -59.05
REMARK 500 6 SER A 31 -26.93 -37.74
REMARK 500 6 MET A 44 -142.35 -75.25
REMARK 500
REMARK 500 THIS ENTRY HAS 261 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 5 0.10 SIDE CHAIN
REMARK 500 1 ARG A 19 0.23 SIDE CHAIN
REMARK 500 1 ARG A 40 0.31 SIDE CHAIN
REMARK 500 1 ARG A 58 0.31 SIDE CHAIN
REMARK 500 2 ARG A 5 0.17 SIDE CHAIN
REMARK 500 2 ARG A 18 0.23 SIDE CHAIN
REMARK 500 2 ARG A 19 0.21 SIDE CHAIN
REMARK 500 2 ARG A 40 0.22 SIDE CHAIN
REMARK 500 2 ARG A 58 0.25 SIDE CHAIN
REMARK 500 3 ARG A 5 0.20 SIDE CHAIN
REMARK 500 3 ARG A 18 0.32 SIDE CHAIN
REMARK 500 3 ARG A 19 0.17 SIDE CHAIN
REMARK 500 3 ARG A 40 0.31 SIDE CHAIN
REMARK 500 3 ARG A 58 0.32 SIDE CHAIN
REMARK 500 4 ARG A 5 0.32 SIDE CHAIN
REMARK 500 4 ARG A 18 0.27 SIDE CHAIN
REMARK 500 4 ARG A 19 0.17 SIDE CHAIN
REMARK 500 4 ARG A 40 0.30 SIDE CHAIN
REMARK 500 4 ARG A 58 0.29 SIDE CHAIN
REMARK 500 5 ARG A 5 0.32 SIDE CHAIN
REMARK 500 5 ARG A 18 0.26 SIDE CHAIN
REMARK 500 5 ARG A 19 0.21 SIDE CHAIN
REMARK 500 5 ARG A 40 0.26 SIDE CHAIN
REMARK 500 5 ARG A 58 0.20 SIDE CHAIN
REMARK 500 6 ARG A 5 0.32 SIDE CHAIN
REMARK 500 6 ARG A 18 0.30 SIDE CHAIN
REMARK 500 6 ARG A 19 0.29 SIDE CHAIN
REMARK 500 6 ARG A 40 0.28 SIDE CHAIN
REMARK 500 6 ARG A 58 0.11 SIDE CHAIN
REMARK 500 7 ARG A 5 0.31 SIDE CHAIN
REMARK 500 7 ARG A 18 0.18 SIDE CHAIN
REMARK 500 7 ARG A 19 0.32 SIDE CHAIN
REMARK 500 7 ARG A 40 0.16 SIDE CHAIN
REMARK 500 7 ARG A 58 0.32 SIDE CHAIN
REMARK 500 8 ARG A 5 0.32 SIDE CHAIN
REMARK 500 8 ARG A 18 0.27 SIDE CHAIN
REMARK 500 8 ARG A 19 0.29 SIDE CHAIN
REMARK 500 8 ARG A 40 0.27 SIDE CHAIN
REMARK 500 8 ARG A 58 0.21 SIDE CHAIN
REMARK 500 9 ARG A 5 0.29 SIDE CHAIN
REMARK 500 9 ARG A 18 0.32 SIDE CHAIN
REMARK 500 9 ARG A 19 0.27 SIDE CHAIN
REMARK 500 9 ARG A 40 0.23 SIDE CHAIN
REMARK 500 9 ARG A 58 0.28 SIDE CHAIN
REMARK 500 10 ARG A 18 0.32 SIDE CHAIN
REMARK 500 10 ARG A 19 0.13 SIDE CHAIN
REMARK 500 10 ARG A 40 0.29 SIDE CHAIN
REMARK 500 10 ARG A 58 0.25 SIDE CHAIN
REMARK 500 11 ARG A 5 0.20 SIDE CHAIN
REMARK 500 11 ARG A 40 0.31 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 142 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1I11 A 1 79 UNP P35710 SOX5_MOUSE 183 261
SEQADV 1I11 GLY A -1 UNP P35710 SEE REMARK 999
SEQADV 1I11 SER A 0 UNP P35710 SEE REMARK 999
SEQRES 1 A 81 GLY SER PRO HIS ILE LYS ARG PRO MET ASN ALA PHE MET
SEQRES 2 A 81 VAL TRP ALA LYS ASP GLU ARG ARG LYS ILE LEU GLN ALA
SEQRES 3 A 81 PHE PRO ASP MET HIS ASN SER ASN ILE SER LYS ILE LEU
SEQRES 4 A 81 GLY SER ARG TRP LYS ALA MET THR ASN LEU GLU LYS GLN
SEQRES 5 A 81 PRO TYR TYR GLU GLU GLN ALA ARG LEU SER LYS GLN HIS
SEQRES 6 A 81 LEU GLU LYS TYR PRO ASP TYR LYS TYR LYS PRO ARG PRO
SEQRES 7 A 81 LYS ARG THR
HELIX 1 1 ALA A 9 PHE A 25 1 17
HELIX 2 2 ASN A 30 ALA A 43 1 14
HELIX 3 3 PRO A 51 TYR A 67 1 17
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 27 2 Bytes