PDB Short entry for 2M9W HEADER TRANSCRIPTION 20-JUN-13 2M9W TITLE SOLUTION NMR STRUCTURE OF TRANSCRIPTION FACTOR GATA-4 FROM HOMO TITLE 2 SAPIENS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET TITLE 3 HR4783B COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR GATA-4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GATA-TYPE 2 ZINC FINGER RESIDUES 262-321; COMPND 5 SYNONYM: GATA-BINDING FACTOR 4; COMPND 6 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: GATA4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PMGK; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15NANO6HT_NESG KEYWDS STRUCTURAL GENOMICS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), KEYWDS 2 PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR X.XU,A.ELETSKY,D.LEE,E.KOHN,H.JANJUA,R.XIAO,T.B.ACTON,J.K.EVERETT, AUTHOR 2 G.T.MONTELIONE,T.SZYPERSKI,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM AUTHOR 3 (NESG) REVDAT 2 14-JUN-23 2M9W 1 REMARK SEQADV LINK REVDAT 1 10-JUL-13 2M9W 0 JRNL AUTH X.XU,A.ELETSKY,D.LEE,E.KOHN,H.JANJUA,R.XIAO,T.ACTON, JRNL AUTH 2 J.K.EVERETT,G.T.MONTELIONE,T.SZYPERSKI JRNL TITL SOLUTION NMR STRUCTURE OF A TRANSCRIPTION FACTOR GATA-4 FROM JRNL TITL 2 HOMO SAPIENS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM JRNL TITL 3 (NESG) TARGET HR4783B JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3, CYANA 3.0, AUTOSTRUCTURE 2.1 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 HUANG, TEJERO, POWERS AND MONTELIONE REMARK 3 (AUTOSTRUCTURE) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE DETERMINATION WAS PERFORMED REMARK 3 BY RUNNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED REMARK 3 CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM REMARK 3 TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN REMARK 3 ITERATIVE REFINEMENT WITH CYANA. THE 20 CONFORMERS OUT OF 100 REMARK 3 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY REMARK 3 SIMULATED ANNEALING IN EXPLICIT WATER BATH USING THE PROGRAM CNS REMARK 3 WITH PARAM19 FORCE FIELD. REMARK 4 REMARK 4 2M9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000103392. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.378 MM [U-100% 13C; U-100% REMARK 210 15N] HR4783B.009, 100 MM SODIUM REMARK 210 CHLORIDE, 5 MM DTT, 10 MM TRIS- REMARK 210 HCL, 50 UM DSS, 0.02 % SODIUM REMARK 210 AZIDE, 50 UM ZINC ION, 90% H2O/ REMARK 210 10% D2O; 0.156 MM [U-5% 13C; U- REMARK 210 100% 15N] HR4783B.009, 100 MM REMARK 210 SODIUM CHLORIDE, 5 MM DTT, 10 MM REMARK 210 TRIS-HCL, 50 UM DSS, 0.02 % REMARK 210 SODIUM AZIDE, 50 UM ZINC ION, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D CT 1H-13C REMARK 210 HSQC ALI; 3D HNCO; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 2D CT 1H-13C HSQC REMARK 210 ARO; 3D SIMUTANEOUS 13C-AROMATIC, REMARK 210 13C-ALIPHATIC,15N EDITED 1H-1H REMARK 210 NOESY; 3D CCH-TOCSY; 3D HBHA(CO) REMARK 210 NH; 2D 1H-15N HSQC_HIS; 2D 1H- REMARK 210 15N HSQC_WIDE; 3D (H)CCH-COSY REMARK 210 ALI; 2D 1H-13C HSQC_METHYL REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.3, CYANA 3.0, REMARK 210 AUTOSTRUCTURE 2.1, AUTOASSIGN REMARK 210 2.3.1, XEASY, VNMRJ 2.3.1, TALOS+ REMARK 210 , PSVS 1.4, PROSA, CSI, CARA REMARK 210 1.8.4 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: NULL 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 ARG A 7 99.72 -53.26 REMARK 500 1 LEU A 11 -172.91 65.14 REMARK 500 1 ASN A 15 -68.13 -171.59 REMARK 500 1 GLN A 17 -1.95 68.73 REMARK 500 1 HIS A 44 -71.51 -124.83 REMARK 500 1 LEU A 50 -71.21 -113.38 REMARK 500 1 ALA A 51 35.81 -94.00 REMARK 500 1 MET A 52 173.47 69.08 REMARK 500 1 ARG A 53 44.66 -80.53 REMARK 500 1 GLU A 55 44.09 -91.71 REMARK 500 2 ASN A 15 -51.06 -172.34 REMARK 500 2 ASN A 27 -168.95 -76.97 REMARK 500 2 LEU A 50 -60.79 -91.23 REMARK 500 2 ALA A 51 -50.36 -139.27 REMARK 500 2 MET A 52 96.85 -68.51 REMARK 500 2 LYS A 54 83.83 -163.40 REMARK 500 2 GLN A 58 -44.76 79.97 REMARK 500 2 ARG A 62 40.75 -97.26 REMARK 500 3 ALA A 5 52.56 -90.43 REMARK 500 3 SER A 6 94.07 -67.01 REMARK 500 3 ASN A 15 -56.45 -171.35 REMARK 500 3 ARG A 53 97.70 -48.99 REMARK 500 3 ARG A 60 110.79 67.45 REMARK 500 4 LEU A 11 170.73 69.26 REMARK 500 4 GLU A 55 -172.60 60.50 REMARK 500 4 ILE A 57 94.68 48.46 REMARK 500 4 GLN A 58 99.22 -61.34 REMARK 500 4 ARG A 62 -54.35 74.45 REMARK 500 5 ASN A 15 -72.18 -103.03 REMARK 500 5 THR A 21 141.98 -170.87 REMARK 500 6 HIS A 2 53.47 -164.75 REMARK 500 6 CYS A 13 103.63 -55.14 REMARK 500 6 ASN A 15 -75.39 -94.16 REMARK 500 6 GLN A 17 69.95 61.66 REMARK 500 6 ARG A 48 109.47 -59.34 REMARK 500 6 LYS A 54 83.14 -69.14 REMARK 500 6 THR A 59 94.79 -63.78 REMARK 500 6 ARG A 62 100.92 63.69 REMARK 500 7 ARG A 7 72.21 55.60 REMARK 500 7 ASN A 27 -169.13 -71.17 REMARK 500 7 ILE A 57 75.97 56.48 REMARK 500 8 VAL A 9 88.07 63.43 REMARK 500 8 THR A 19 -47.20 67.63 REMARK 500 8 HIS A 44 -71.20 -129.14 REMARK 500 8 LEU A 50 -69.98 -100.07 REMARK 500 8 LYS A 61 24.74 -154.82 REMARK 500 9 HIS A 2 84.89 -68.09 REMARK 500 9 MET A 3 114.96 -161.49 REMARK 500 9 SER A 6 94.58 -66.91 REMARK 500 9 ASN A 15 -67.41 -175.38 REMARK 500 REMARK 500 THIS ENTRY HAS 136 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 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 13 SG REMARK 620 2 CYS A 16 SG 100.2 REMARK 620 3 CYS A 34 SG 124.1 111.4 REMARK 620 4 CYS A 37 SG 109.8 106.7 103.7 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 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19312 RELATED DB: BMRB REMARK 900 RELATED ID: NESG-HR4783B RELATED DB: TARGETTRACK DBREF 2M9W A 4 63 UNP P43694 GATA4_HUMAN 262 321 SEQADV 2M9W SER A 1 UNP P43694 EXPRESSION TAG SEQADV 2M9W HIS A 2 UNP P43694 EXPRESSION TAG SEQADV 2M9W MET A 3 UNP P43694 EXPRESSION TAG SEQRES 1 A 63 SER HIS MET SER ALA SER ARG ARG VAL GLY LEU SER CYS SEQRES 2 A 63 ALA ASN CYS GLN THR THR THR THR THR LEU TRP ARG ARG SEQRES 3 A 63 ASN ALA GLU GLY GLU PRO VAL CYS ASN ALA CYS GLY LEU SEQRES 4 A 63 TYR MET LYS LEU HIS GLY VAL PRO ARG PRO LEU ALA MET SEQRES 5 A 63 ARG LYS GLU GLY ILE GLN THR ARG LYS ARG LYS HET ZN A 101 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ASN A 35 HIS A 44 1 10 SHEET 1 A 2 TRP A 24 ARG A 26 0 SHEET 2 A 2 PRO A 32 CYS A 34 -1 O VAL A 33 N ARG A 25 LINK SG CYS A 13 ZN ZN A 101 1555 1555 1.93 LINK SG CYS A 16 ZN ZN A 101 1555 1555 1.86 LINK SG CYS A 34 ZN ZN A 101 1555 1555 1.82 LINK SG CYS A 37 ZN ZN A 101 1555 1555 1.92 SITE 1 AC1 4 CYS A 13 CYS A 16 CYS A 34 CYS A 37 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