10 20 30 40 50 60 70 80 1VA2 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION 07-FEB-04 1VA2
TITLE SOLUTION STRUCTURE OF TRANSCRIPTION FACTOR SP1 DNA BINDING TITLE 2 DOMAIN (ZINC FINGER 2)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR SP1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC FINGER 2; 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 KEYWDS 2 PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 31
MDLTYP MINIMIZED AVERAGE
AUTHOR S.OKA,Y.SHIRAISHI,T.YOSHIDA,T.OHKUBO,Y.SUGIURA,Y.KOBAYASHI
REVDAT 2 24-FEB-09 1VA2 1 VERSN REVDAT 1 08-FEB-05 1VA2 0
JRNL AUTH S.OKA,Y.SHIRAISHI,T.YOSHIDA,T.OHKUBO,Y.SUGIURA, JRNL AUTH 2 Y.KOBAYASHI JRNL TITL NMR STRUCTURE OF TRANSCRIPTION FACTOR SP1 DNA JRNL TITL 2 BINDING DOMAIN JRNL REF BIOCHEMISTRY V. 43 16027 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15609997 JRNL DOI 10.1021/BI048438P
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, REMARK 3 RICE,SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1VA2 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 RCSB ID CODE IS RCSB006395.
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 REMARK 210 NACL; 1MM DTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY, 3D_ REMARK 210 15N-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 : CNS 1.1, NMRPIPE 2.1, NMRVIEW REMARK 210 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 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 PRO A 566 46.91 -83.22 REMARK 500 1 TRP A 571 103.83 -56.39 REMARK 500 1 GLU A 594 -44.68 -163.35 REMARK 500 2 GLU A 594 -80.25 62.29 REMARK 500 3 TRP A 571 98.02 -63.86 REMARK 500 3 GLU A 594 97.02 57.23 REMARK 500 4 PRO A 566 49.73 -81.66 REMARK 500 4 GLU A 594 -66.26 -91.58 REMARK 500 5 PRO A 566 47.16 -83.84 REMARK 500 5 TRP A 571 -162.74 39.45 REMARK 500 5 TYR A 573 38.35 -172.84 REMARK 500 6 HIS A 591 -66.99 -95.77 REMARK 500 7 PRO A 566 47.30 -84.22 REMARK 500 7 TRP A 571 -163.15 40.94 REMARK 500 7 TYR A 573 38.78 -172.33 REMARK 500 7 THR A 592 107.98 58.62 REMARK 500 8 CYS A 569 -170.45 -56.83 REMARK 500 8 TRP A 571 177.82 -51.08 REMARK 500 9 PRO A 566 47.63 -81.70 REMARK 500 9 TRP A 571 176.53 -52.45 REMARK 500 9 TYR A 573 83.51 -167.42 REMARK 500 9 THR A 592 98.51 53.38 REMARK 500 9 GLU A 594 -74.82 -62.50 REMARK 500 10 TRP A 571 172.69 -49.25 REMARK 500 11 PRO A 566 47.61 -82.60 REMARK 500 11 TRP A 571 171.57 -48.31 REMARK 500 11 TYR A 573 82.01 -164.38 REMARK 500 12 PRO A 566 43.89 -83.53 REMARK 500 12 TRP A 571 -163.79 39.94 REMARK 500 12 TYR A 573 35.04 -171.64 REMARK 500 13 PRO A 566 47.78 -84.34 REMARK 500 13 THR A 570 37.02 -94.46 REMARK 500 13 TYR A 573 75.39 -162.47 REMARK 500 13 GLU A 594 73.73 60.87 REMARK 500 14 TRP A 571 -163.83 40.66 REMARK 500 14 TYR A 573 42.81 -171.71 REMARK 500 14 THR A 592 -167.72 45.41 REMARK 500 15 TRP A 571 -179.75 -52.25 REMARK 500 15 TYR A 573 79.55 -163.76 REMARK 500 16 PRO A 566 63.78 -68.77 REMARK 500 16 LYS A 576 117.72 -160.88 REMARK 500 17 TRP A 571 -176.30 -54.05 REMARK 500 17 TYR A 573 76.03 -158.70 REMARK 500 17 GLU A 594 85.11 60.45 REMARK 500 18 PRO A 566 58.27 -66.90 REMARK 500 18 TRP A 571 168.91 -47.44 REMARK 500 18 TYR A 573 82.72 -161.51 REMARK 500 18 THR A 592 91.49 43.35 REMARK 500 19 PRO A 566 60.98 -69.22 REMARK 500 19 TRP A 571 167.30 -46.24 REMARK 500 19 TYR A 573 87.34 -163.34 REMARK 500 20 PRO A 566 47.93 -83.42 REMARK 500 20 THR A 570 37.85 -92.90 REMARK 500 20 TYR A 573 73.00 -161.14 REMARK 500 20 THR A 592 -45.60 -159.35 REMARK 500 21 PRO A 566 49.33 -81.71 REMARK 500 21 TYR A 573 86.32 -163.90 REMARK 500 22 TRP A 571 171.64 -50.23 REMARK 500 22 TYR A 573 84.19 -165.34 REMARK 500 23 THR A 570 33.92 -92.83 REMARK 500 23 TRP A 571 -177.43 -67.22 REMARK 500 23 TYR A 573 77.64 -158.20 REMARK 500 24 THR A 592 -170.13 52.88 REMARK 500 25 PRO A 566 47.36 -83.02 REMARK 500 25 THR A 570 34.90 -93.77 REMARK 500 25 TYR A 573 75.35 -161.94 REMARK 500 25 GLU A 594 165.84 61.52 REMARK 500 26 PRO A 566 80.64 -66.15 REMARK 500 26 THR A 570 35.93 -94.56 REMARK 500 26 TYR A 573 76.05 -166.64 REMARK 500 27 THR A 570 36.21 -84.58 REMARK 500 27 TRP A 571 -177.30 -68.16 REMARK 500 27 TYR A 573 72.08 -163.62 REMARK 500 27 HIS A 591 103.02 -162.53 REMARK 500 28 PRO A 566 48.00 -81.20 REMARK 500 28 TRP A 571 -98.97 -44.75 REMARK 500 28 TYR A 573 52.89 -154.81 REMARK 500 28 LYS A 576 114.16 -169.39 REMARK 500 29 PRO A 566 49.70 -83.70 REMARK 500 29 TRP A 571 -99.86 -54.03 REMARK 500 29 TYR A 573 79.83 -179.20 REMARK 500 29 GLU A 594 156.49 60.94 REMARK 500 30 PRO A 566 47.86 -82.05 REMARK 500 30 THR A 570 39.46 -85.18 REMARK 500 30 TYR A 573 52.47 -157.23 REMARK 500 30 HIS A 591 28.10 -172.23 REMARK 500 30 GLU A 594 31.63 -147.40 REMARK 500 31 PRO A 566 45.87 -84.87 REMARK 500 31 TRP A 571 -86.53 -40.15 REMARK 500 31 TYR A 573 60.47 -163.88 REMARK 500 31 HIS A 591 -71.26 -105.34 REMARK 500 31 GLU A 594 74.34 -154.38 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 1 ZN A 100 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 569 SG REMARK 620 2 CYS A 574 SG 91.5 REMARK 620 3 HIS A 587 NE2 128.8 125.9 REMARK 620 4 HIS A 591 NE2 124.9 86.6 94.2 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: 1VA3 RELATED DB: PDB REMARK 900 THE SAME PROTEIN, ZINC FINGER 3 DOMAIN
DBREF 1VA2 A 565 595 UNP P08047 SP1_HUMAN 654 684
SEQRES 1 A 31 ARG PRO PHE MET CYS THR TRP SER TYR CYS GLY LYS ARG SEQRES 2 A 31 PHE THR ARG SER ASP GLU LEU GLN ARG HIS LYS ARG THR SEQRES 3 A 31 HIS THR GLY GLU LYS
HET ZN A 100 1
HETNAM ZN ZINC ION
FORMUL 2 ZN ZN 2+
HELIX 1 1 ARG A 580 ARG A 589 1 10
SHEET 1 A 2 PHE A 567 MET A 568 0 SHEET 2 A 2 ARG A 577 PHE A 578 -1 O PHE A 578 N PHE A 567
LINK ZN ZN A 100 SG CYS A 569 1555 1555 2.33 LINK ZN ZN A 100 SG CYS A 574 1555 1555 2.34 LINK ZN ZN A 100 NE2 HIS A 587 1555 1555 2.06 LINK ZN ZN A 100 NE2 HIS A 591 1555 1555 2.02
SITE 1 AC1 4 CYS A 569 CYS A 574 HIS A 587 HIS A 591
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