PDB Short entry for 1VA3 HEADER TRANSCRIPTION 07-FEB-04 1VA3 TITLE SOLUTION STRUCTURE OF TRANSCRIPTION FACTOR SP1 DNA BINDING DOMAIN TITLE 2 (ZINC FINGER 3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR SP1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC FINGER 3; 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 GENE: SP1; 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: PEVSP1 KEYWDS C2H2 TYPE ZINC FINGER, TRANSCRIPTION FACTOR, DNA-BINDING PROTEIN, KEYWDS 2 TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 31 MDLTYP MINIMIZED AVERAGE AUTHOR S.OKA,Y.SHIRAISHI,T.YOSHIDA,T.OHKUBO,Y.SUGIURA,Y.KOBAYASHI REVDAT 4 27-DEC-23 1VA3 1 REMARK REVDAT 3 02-MAR-22 1VA3 1 REMARK REVDAT 2 24-FEB-09 1VA3 1 VERSN REVDAT 1 08-FEB-05 1VA3 0 JRNL AUTH S.OKA,Y.SHIRAISHI,T.YOSHIDA,T.OHKUBO,Y.SUGIURA,Y.KOBAYASHI JRNL TITL NMR STRUCTURE OF TRANSCRIPTION FACTOR SP1 DNA BINDING DOMAIN JRNL REF BIOCHEMISTRY V. 43 16027 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15609997 JRNL DOI 10.1021/BI048438P REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE REMARK 3 -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON, REMARK 3 WARREN (CNS), BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VA3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000006396. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 10MM TRIS-D, 50MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM SP1 DNA-BINDING DOMAIN U REMARK 210 -15N/13C; 10MM TRIS-D; 50MM NACL; REMARK 210 1MM DTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, NMRVIEW 5.0.4 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 31 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 31 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 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 3 ASN A 621 155.97 61.01 REMARK 500 4 GLN A 620 101.55 55.40 REMARK 500 6 PHE A 597 84.49 -154.63 REMARK 500 6 ASN A 621 -47.93 -142.18 REMARK 500 7 PHE A 597 -74.64 -163.41 REMARK 500 7 ALA A 598 -177.77 57.53 REMARK 500 7 LYS A 604 139.32 -176.35 REMARK 500 7 ARG A 608 -168.48 -165.04 REMARK 500 9 ARG A 608 120.35 -172.24 REMARK 500 9 GLN A 620 95.48 57.94 REMARK 500 9 ASN A 621 -70.60 -88.78 REMARK 500 10 ASN A 621 94.43 60.08 REMARK 500 11 ASN A 621 -178.61 -64.37 REMARK 500 12 ARG A 608 -179.37 -174.77 REMARK 500 13 LYS A 596 66.23 -165.67 REMARK 500 13 ALA A 598 173.13 58.85 REMARK 500 13 ARG A 608 142.01 -175.96 REMARK 500 13 ASN A 621 85.01 61.57 REMARK 500 15 PHE A 597 107.06 57.75 REMARK 500 17 PHE A 597 -57.75 -141.20 REMARK 500 17 ALA A 598 168.88 61.12 REMARK 500 17 MET A 607 30.17 -97.92 REMARK 500 18 LYS A 596 43.85 -95.56 REMARK 500 18 GLN A 620 -72.19 -58.06 REMARK 500 18 ASN A 621 -50.02 -151.36 REMARK 500 18 LYS A 622 99.87 -68.67 REMARK 500 19 ARG A 608 138.77 -173.58 REMARK 500 21 MET A 607 31.43 -98.42 REMARK 500 21 ARG A 608 126.57 -176.44 REMARK 500 21 ASN A 621 103.11 59.85 REMARK 500 22 PHE A 597 86.63 59.08 REMARK 500 23 ASN A 621 108.87 60.51 REMARK 500 25 LYS A 596 30.71 -147.32 REMARK 500 25 CYS A 599 108.03 -57.18 REMARK 500 27 ASN A 621 -61.76 -93.92 REMARK 500 28 LYS A 596 60.94 -104.94 REMARK 500 29 PHE A 597 57.18 -97.78 REMARK 500 29 PHE A 606 -43.68 -136.35 REMARK 500 29 ARG A 608 99.20 -160.80 REMARK 500 30 ASN A 621 -47.25 -135.56 REMARK 500 31 LYS A 596 31.13 -98.82 REMARK 500 31 MET A 607 30.06 -98.90 REMARK 500 31 GLN A 620 80.59 -64.98 REMARK 500 31 ASN A 621 91.68 -68.68 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 100 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 599 SG REMARK 620 2 CYS A 602 SG 112.7 REMARK 620 3 HIS A 615 NE2 114.5 96.2 REMARK 620 4 HIS A 619 NE2 123.4 103.6 102.6 REMARK 620 N 1 2 3 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 100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VA1 RELATED DB: PDB REMARK 900 THE SAME PROTEIN, ZINC FINGER 1 DOMAIN REMARK 900 RELATED ID: 1VA2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN, ZINC FINGER 2 DOMAIN DBREF 1VA3 A 595 623 UNP P08047 SP1_HUMAN 684 712 SEQRES 1 A 29 LYS LYS PHE ALA CYS PRO GLU CYS PRO LYS ARG PHE MET SEQRES 2 A 29 ARG SER ASP HIS LEU SER LYS HIS ILE LYS THR HIS GLN SEQRES 3 A 29 ASN LYS LYS HET ZN A 100 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 SER A 609 GLN A 620 1 12 LINK ZN ZN A 100 SG CYS A 599 1555 1555 2.32 LINK ZN ZN A 100 SG CYS A 602 1555 1555 2.30 LINK ZN ZN A 100 NE2 HIS A 615 1555 1555 2.01 LINK ZN ZN A 100 NE2 HIS A 619 1555 1555 2.01 SITE 1 AC1 4 CYS A 599 CYS A 602 HIS A 615 HIS A 619 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