HEADER DNA BINDING PROTEIN 22-MAR-02 1L8Y TITLE SOLUTION STRUCTURE OF HMG BOX 5 IN HUMAN UPSTREAM BINDING FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPSTREAM BINDING FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HMG BOX 5 DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-22B KEYWDS HUBF, HMG BOX 5, DNA BINDING DOMAIN, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR W.YANG,Y.XU,J.WU,W.ZENG,Y.SHI REVDAT 6 29-MAY-24 1L8Y 1 REMARK REVDAT 5 21-DEC-22 1L8Y 1 SEQADV REVDAT 4 23-FEB-22 1L8Y 1 REMARK SEQADV REVDAT 3 24-FEB-09 1L8Y 1 VERSN REVDAT 2 24-JUN-03 1L8Y 1 JRNL REVDAT 1 05-JUN-02 1L8Y 0 JRNL AUTH W.YANG,Y.XU,J.WU,W.ZENG,Y.SHI JRNL TITL SOLUTION STRUCTURE AND DNA BINDING PROPERTY OF THE FIFTH HMG JRNL TITL 2 BOX DOMAIN IN COMPARISON WITH THE FIRST HMG BOX DOMAIN IN JRNL TITL 3 HUMAN UPSTREAM BINDING FACTOR JRNL REF BIOCHEMISTRY V. 42 1930 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12590579 JRNL DOI 10.1021/BI026372X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPP, CNS REMARK 3 AUTHORS : F.DELAGIO AND A.BAX (NMRPIPP), A.T.BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON THE TOTAL REMARK 3 NUMBER CONSTRAINTS OF 1220, INCLUDING 1098 NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, 104 DIHEDRAL ANGLE CONSTRAINTS, 18 HYDROGEN BOND REMARK 3 CONSTRAINTS. REMARK 4 REMARK 4 1L8Y COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1000015754. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 45 MM NAPO4 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3MM HUBF HMG BOX 5, U-15N, 13C; REMARK 210 45MM NAPO4; 3MM HUBF HMG BOX 5, REMARK 210 U-15N, 13C; 45MM NAPO4 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PIPP, CNS 1.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS 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 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 MET A 0 REMARK 465 HIS A 85 REMARK 465 HIS A 86 REMARK 465 HIS A 87 REMARK 465 HIS A 88 REMARK 465 HIS A 89 REMARK 465 HIS A 90 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-30 REMARK 470 RES CSSEQI ATOMS REMARK 470 GLU A 84 O 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 ASP A 29 H ALA A 33 1.58 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 LYS A 2 -74.49 172.53 REMARK 500 1 SER A 6 86.84 57.31 REMARK 500 1 PRO A 7 -149.38 -56.11 REMARK 500 1 LYS A 8 28.75 -158.00 REMARK 500 1 ARG A 9 -88.75 50.35 REMARK 500 1 ALA A 10 -77.01 -74.03 REMARK 500 1 ILE A 19 -34.75 -34.48 REMARK 500 1 ASN A 28 31.47 114.71 REMARK 500 1 ARG A 30 -55.26 -18.79 REMARK 500 1 GLU A 45 -158.37 60.54 REMARK 500 1 GLU A 48 -76.02 -75.71 REMARK 500 1 LYS A 49 -70.84 -28.53 REMARK 500 1 GLU A 66 -76.42 -68.96 REMARK 500 1 ARG A 71 38.50 -95.67 REMARK 500 1 ALA A 76 30.38 -154.18 REMARK 500 1 THR A 77 -41.07 -174.84 REMARK 500 1 LYS A 81 92.63 38.25 REMARK 500 1 LYS A 82 70.86 -69.07 REMARK 500 2 LYS A 2 80.08 47.42 REMARK 500 2 LEU A 3 -55.65 -149.53 REMARK 500 2 PRO A 4 -75.96 -54.00 REMARK 500 2 GLU A 5 67.42 10.17 REMARK 500 2 PRO A 7 171.67 -49.94 REMARK 500 2 LYS A 8 36.60 -157.33 REMARK 500 2 ARG A 9 -90.55 47.27 REMARK 500 2 ALA A 10 -81.77 -70.41 REMARK 500 2 LYS A 27 90.06 74.69 REMARK 500 2 ASN A 28 21.57 89.78 REMARK 500 2 ARG A 30 -55.17 -19.52 REMARK 500 2 GLU A 45 -159.00 62.23 REMARK 500 2 LYS A 49 -75.90 -34.75 REMARK 500 2 GLU A 66 -76.50 -74.57 REMARK 500 2 ARG A 71 31.33 -99.74 REMARK 500 2 PRO A 74 32.76 -91.73 REMARK 500 2 SER A 80 -32.99 -179.89 REMARK 500 3 LYS A 2 -143.25 -68.10 REMARK 500 3 PRO A 7 -147.58 -57.05 REMARK 500 3 LYS A 8 34.45 -163.41 REMARK 500 3 ARG A 9 -89.18 47.79 REMARK 500 3 ALA A 10 -80.03 -72.23 REMARK 500 3 ILE A 19 -34.36 -37.18 REMARK 500 3 LYS A 27 68.93 77.29 REMARK 500 3 ASN A 28 38.71 96.35 REMARK 500 3 ARG A 30 -25.32 -30.28 REMARK 500 3 VAL A 31 -37.43 -34.97 REMARK 500 3 GLU A 45 -160.19 52.47 REMARK 500 3 LYS A 49 -78.82 -37.58 REMARK 500 3 GLU A 66 -78.24 -68.24 REMARK 500 3 ALA A 72 50.10 -157.60 REMARK 500 3 PRO A 74 37.27 -93.11 REMARK 500 REMARK 500 THIS ENTRY HAS 625 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1L8Z RELATED DB: PDB REMARK 900 1L8Z CONTAINS MINIMIZED AVERAGE STRUCTURE OF THE SAME PROTEIN DBREF 1L8Y A 1 82 UNP P17480 UBF1_HUMAN 479 560 SEQADV 1L8Y MET A 0 UNP P17480 INITIATING METHIONINE SEQADV 1L8Y LEU A 83 UNP P17480 EXPRESSION TAG SEQADV 1L8Y GLU A 84 UNP P17480 EXPRESSION TAG SEQADV 1L8Y HIS A 85 UNP P17480 EXPRESSION TAG SEQADV 1L8Y HIS A 86 UNP P17480 EXPRESSION TAG SEQADV 1L8Y HIS A 87 UNP P17480 EXPRESSION TAG SEQADV 1L8Y HIS A 88 UNP P17480 EXPRESSION TAG SEQADV 1L8Y HIS A 89 UNP P17480 EXPRESSION TAG SEQADV 1L8Y HIS A 90 UNP P17480 EXPRESSION TAG SEQRES 1 A 91 MET GLY LYS LEU PRO GLU SER PRO LYS ARG ALA GLU GLU SEQRES 2 A 91 ILE TRP GLN GLN SER VAL ILE GLY ASP TYR LEU ALA ARG SEQRES 3 A 91 PHE LYS ASN ASP ARG VAL LYS ALA LEU LYS ALA MET GLU SEQRES 4 A 91 MET THR TRP ASN ASN MET GLU LYS LYS GLU LYS LEU MET SEQRES 5 A 91 TRP ILE LYS LYS ALA ALA GLU ASP GLN LYS ARG TYR GLU SEQRES 6 A 91 ARG GLU LEU SER GLU MET ARG ALA PRO PRO ALA ALA THR SEQRES 7 A 91 ASN SER SER LYS LYS LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 ARG A 9 PHE A 26 1 18 HELIX 2 2 ASP A 29 ASN A 43 1 15 HELIX 3 3 MET A 44 LYS A 46 5 3 HELIX 4 4 LYS A 47 GLU A 69 1 23 HELIX 5 5 ALA A 72 ALA A 76 5 5 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