PDB Short entry for 1I11 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