PDB Short entry for 1VA1 HEADER TRANSCRIPTION 07-FEB-04 1VA1 TITLE SOLUTION STRUCTURE OF TRANSCRIPTION FACTOR SP1 DNA BINDING DOMAIN TITLE 2 (ZINC FINGER 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR SP1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC FINGER 1; 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 1VA1 1 REMARK REVDAT 3 02-MAR-22 1VA1 1 REMARK SEQADV REVDAT 2 24-FEB-09 1VA1 1 VERSN REVDAT 1 08-FEB-05 1VA1 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 1VA1 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_1000006394. 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 1 CYS A 539 96.25 -66.11 REMARK 500 2 LYS A 535 158.22 60.64 REMARK 500 2 HIS A 540 30.55 -97.61 REMARK 500 2 GLN A 542 83.07 -62.58 REMARK 500 2 LYS A 546 -164.98 -100.10 REMARK 500 2 THR A 562 36.33 -97.31 REMARK 500 3 GLN A 536 -178.65 60.07 REMARK 500 3 CYS A 539 91.43 -65.31 REMARK 500 3 GLU A 564 -48.35 -146.58 REMARK 500 4 PRO A 531 98.74 -50.90 REMARK 500 4 HIS A 540 51.03 -115.96 REMARK 500 4 CYS A 544 -174.97 -68.75 REMARK 500 5 CYS A 544 -168.94 -107.79 REMARK 500 5 THR A 562 30.62 -97.78 REMARK 500 5 GLU A 564 -79.32 63.02 REMARK 500 6 LYS A 535 157.37 62.53 REMARK 500 6 GLN A 536 126.04 63.26 REMARK 500 6 HIS A 540 33.87 -96.80 REMARK 500 6 GLU A 564 -47.35 -146.24 REMARK 500 7 LYS A 535 -178.53 60.07 REMARK 500 7 CYS A 539 86.29 -59.91 REMARK 500 8 CYS A 539 97.02 -68.90 REMARK 500 9 LYS A 546 -172.42 -67.92 REMARK 500 10 LYS A 535 92.25 43.48 REMARK 500 11 LYS A 535 158.22 60.64 REMARK 500 11 HIS A 540 30.55 -97.61 REMARK 500 11 GLN A 542 83.07 -62.58 REMARK 500 11 LYS A 546 -164.98 -100.10 REMARK 500 11 THR A 562 36.33 -97.31 REMARK 500 12 GLN A 542 89.35 -58.89 REMARK 500 12 VAL A 547 87.00 57.12 REMARK 500 12 GLU A 564 32.32 -161.58 REMARK 500 13 GLN A 536 131.02 -172.91 REMARK 500 13 CYS A 539 98.49 -62.14 REMARK 500 13 CYS A 544 -165.72 -115.79 REMARK 500 13 VAL A 547 86.53 53.71 REMARK 500 14 HIS A 540 35.96 -96.65 REMARK 500 15 CYS A 539 93.15 -64.04 REMARK 500 15 CYS A 544 -168.16 -110.70 REMARK 500 15 LYS A 546 -171.45 -60.76 REMARK 500 15 THR A 562 -178.28 56.06 REMARK 500 16 ASP A 530 98.91 60.60 REMARK 500 16 CYS A 544 -165.16 -119.08 REMARK 500 17 CYS A 544 -167.03 -64.91 REMARK 500 17 VAL A 547 82.96 54.17 REMARK 500 17 GLU A 564 165.14 60.11 REMARK 500 18 PRO A 531 108.32 -51.87 REMARK 500 18 GLU A 564 -45.95 -155.83 REMARK 500 19 CYS A 544 -166.01 -64.98 REMARK 500 19 VAL A 547 99.31 57.04 REMARK 500 REMARK 500 THIS ENTRY HAS 88 RAMACHANDRAN OUTLIERS. 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 539 SG REMARK 620 2 CYS A 544 SG 121.8 REMARK 620 3 HIS A 557 NE2 89.5 129.2 REMARK 620 4 HIS A 561 NE2 88.9 120.9 95.9 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: 1VA2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN, ZINC FINGER 2 DOMAIN REMARK 900 RELATED ID: 1VA3 RELATED DB: PDB REMARK 900 THE SAME PROTEIN, ZINC FINGER 3 DOMAIN DBREF 1VA1 A 530 565 UNP P08047 SP1_HUMAN 619 654 SEQADV 1VA1 MET A 1 UNP P08047 INITIATING METHIONINE SEQRES 1 A 37 MET ASP PRO GLY LYS LYS LYS GLN HIS ILE CYS HIS ILE SEQRES 2 A 37 GLN GLY CYS GLY LYS VAL TYR GLY LYS THR SER HIS LEU SEQRES 3 A 37 ARG ALA HIS LEU ARG TRP HIS THR GLY GLU ARG HET ZN A 100 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 LYS A 550 GLY A 563 1 14 SHEET 1 A 2 HIS A 537 ILE A 538 0 SHEET 2 A 2 VAL A 547 TYR A 548 -1 O TYR A 548 N HIS A 537 LINK ZN ZN A 100 SG CYS A 539 1555 1555 2.30 LINK ZN ZN A 100 SG CYS A 544 1555 1555 2.31 LINK ZN ZN A 100 NE2 HIS A 557 1555 1555 2.01 LINK ZN ZN A 100 NE2 HIS A 561 1555 1555 2.02 SITE 1 AC1 4 CYS A 539 CYS A 544 HIS A 557 HIS A 561 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