PDB Short entry for 5O9B HEADER TRANSCRIPTION 16-JUN-17 5O9B TITLE SOLUTION NMR STRUCTURE OF HUMAN GATA2 C-TERMINAL ZINC FINGER DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOTHELIAL TRANSCRIPTION FACTOR GATA-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GATA-BINDING PROTEIN 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: GATA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GATA, TRANSCRIPTION FACTOR, HAEMATOPOEISIS, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.S.NURMOHAMED,R.W.BROADHURST,G.MAY,T.ENVER REVDAT 3 14-JUN-23 5O9B 1 REMARK REVDAT 2 08-MAY-19 5O9B 1 REMARK REVDAT 1 06-FEB-19 5O9B 0 JRNL AUTH S.S.NURMOHAMED,R.W.BROADHURST,G.MAY,T.ENVER JRNL TITL SOLUTION NMR STRUCTURE OF HUMAN GATA2 C-TERMINAL ZINC FINGER JRNL TITL 2 DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5O9B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005001. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 PA REMARK 210 SAMPLE CONTENTS : 10 MG/L [U-99% 13C; U-99% 15N] REMARK 210 GATA2 ZINC FINGER 2, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D HBHA(CO) REMARK 210 NH; 3D 1H-15N TOCSY; 2D 1H-15N REMARK 210 HSQC; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX500; DRX800 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 2.3, CCPNMR ANALYSIS 2.4.1 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 8 TYR A 34 CE1 TYR A 34 CZ 0.101 REMARK 500 8 TYR A 34 CZ TYR A 34 CE2 -0.107 REMARK 500 18 TYR A 34 CE1 TYR A 34 CZ 0.082 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 ALA A -17 47.02 -157.36 REMARK 500 1 GLN A -2 -82.19 67.98 REMARK 500 1 PRO A 0 -96.90 -93.73 REMARK 500 1 ARG A 2 9.35 -151.29 REMARK 500 1 ALA A 3 -99.15 68.02 REMARK 500 1 ALA A 8 24.12 -61.47 REMARK 500 1 ASN A 9 -51.17 -154.96 REMARK 500 1 GLN A 11 13.00 47.01 REMARK 500 1 LEU A 44 -72.95 -154.92 REMARK 500 1 THR A 45 -156.74 -131.56 REMARK 500 1 MET A 46 -92.80 -80.76 REMARK 500 1 LYS A 47 -31.39 -140.93 REMARK 500 2 HIS A -13 -64.48 -151.55 REMARK 500 2 HIS A -12 75.24 -176.02 REMARK 500 2 SER A -9 40.99 -86.94 REMARK 500 2 GLN A -2 -72.12 -165.20 REMARK 500 2 PRO A 0 174.64 -59.33 REMARK 500 2 ARG A 2 22.05 -156.64 REMARK 500 2 ALA A 3 -89.77 61.26 REMARK 500 2 THR A 5 -169.14 -104.09 REMARK 500 2 ALA A 8 23.83 -62.61 REMARK 500 2 ASN A 9 -45.64 -157.11 REMARK 500 2 GLN A 11 21.63 39.79 REMARK 500 2 LEU A 44 -73.46 -150.94 REMARK 500 2 THR A 45 -159.49 -139.47 REMARK 500 2 MET A 46 -154.07 -98.74 REMARK 500 3 HIS A -16 109.44 -58.98 REMARK 500 3 PRO A 0 -146.78 -89.88 REMARK 500 3 ARG A 1 -163.37 -122.74 REMARK 500 3 ARG A 2 -15.02 179.44 REMARK 500 3 ALA A 3 -94.08 66.38 REMARK 500 3 ALA A 8 24.94 -61.88 REMARK 500 3 ASN A 9 -43.45 -160.18 REMARK 500 3 GLN A 11 17.84 44.17 REMARK 500 3 LEU A 44 -71.50 -166.26 REMARK 500 3 THR A 45 -97.64 50.76 REMARK 500 3 LYS A 47 -68.72 70.81 REMARK 500 4 HIS A -12 -77.80 -79.76 REMARK 500 4 HIS A -11 150.66 67.00 REMARK 500 4 LEU A -7 43.31 -80.21 REMARK 500 4 PHE A -3 -33.65 -146.54 REMARK 500 4 PRO A 0 -144.12 -92.20 REMARK 500 4 ARG A 2 14.45 -176.33 REMARK 500 4 ALA A 3 -95.74 65.89 REMARK 500 4 ALA A 8 24.11 -61.32 REMARK 500 4 ASN A 9 -49.18 -156.45 REMARK 500 4 GLN A 11 23.00 38.64 REMARK 500 4 THR A 14 74.28 -102.56 REMARK 500 4 LEU A 44 -158.18 -121.69 REMARK 500 4 THR A 45 -157.76 -139.45 REMARK 500 REMARK 500 THIS ENTRY HAS 275 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 TYR A 35 0.05 SIDE CHAIN REMARK 500 4 TYR A 35 0.06 SIDE CHAIN REMARK 500 7 TYR A 34 0.09 SIDE CHAIN REMARK 500 12 TYR A 35 0.06 SIDE CHAIN REMARK 500 14 TYR A 34 0.06 SIDE CHAIN REMARK 500 15 TYR A 34 0.06 SIDE CHAIN REMARK 500 18 TYR A 34 0.08 SIDE CHAIN 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 7 SG REMARK 620 2 CYS A 10 SG 107.7 REMARK 620 3 CYS A 28 SG 107.7 109.1 REMARK 620 4 CYS A 31 SG 105.8 116.6 109.6 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 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34149 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF HUMAN GATA2 C-TERMINAL ZINC FINGER DOMAIN DBREF 5O9B A 1 49 UNP P23769 GATA2_HUMAN 343 391 SEQADV 5O9B MET A -18 UNP P23769 INITIATING METHIONINE SEQADV 5O9B ALA A -17 UNP P23769 EXPRESSION TAG SEQADV 5O9B HIS A -16 UNP P23769 EXPRESSION TAG SEQADV 5O9B HIS A -15 UNP P23769 EXPRESSION TAG SEQADV 5O9B HIS A -14 UNP P23769 EXPRESSION TAG SEQADV 5O9B HIS A -13 UNP P23769 EXPRESSION TAG SEQADV 5O9B HIS A -12 UNP P23769 EXPRESSION TAG SEQADV 5O9B HIS A -11 UNP P23769 EXPRESSION TAG SEQADV 5O9B SER A -10 UNP P23769 EXPRESSION TAG SEQADV 5O9B SER A -9 UNP P23769 EXPRESSION TAG SEQADV 5O9B GLY A -8 UNP P23769 EXPRESSION TAG SEQADV 5O9B LEU A -7 UNP P23769 EXPRESSION TAG SEQADV 5O9B GLU A -6 UNP P23769 EXPRESSION TAG SEQADV 5O9B VAL A -5 UNP P23769 EXPRESSION TAG SEQADV 5O9B LEU A -4 UNP P23769 EXPRESSION TAG SEQADV 5O9B PHE A -3 UNP P23769 EXPRESSION TAG SEQADV 5O9B GLN A -2 UNP P23769 EXPRESSION TAG SEQADV 5O9B GLY A -1 UNP P23769 EXPRESSION TAG SEQADV 5O9B PRO A 0 UNP P23769 EXPRESSION TAG SEQRES 1 A 68 MET ALA HIS HIS HIS HIS HIS HIS SER SER GLY LEU GLU SEQRES 2 A 68 VAL LEU PHE GLN GLY PRO ARG ARG ALA GLY THR CYS CYS SEQRES 3 A 68 ALA ASN CYS GLN THR THR THR THR THR LEU TRP ARG ARG SEQRES 4 A 68 ASN ALA ASN GLY ASP PRO VAL CYS ASN ALA CYS GLY LEU SEQRES 5 A 68 TYR TYR LYS LEU HIS ASN VAL ASN ARG PRO LEU THR MET SEQRES 6 A 68 LYS LYS GLU HET ZN A 101 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 AA1 CYS A 28 ASN A 39 1 12 SHEET 1 AA1 2 ARG A 19 ARG A 20 0 SHEET 2 AA1 2 PRO A 26 VAL A 27 -1 O VAL A 27 N ARG A 19 LINK SG CYS A 7 ZN ZN A 101 1555 1555 2.29 LINK SG CYS A 10 ZN ZN A 101 1555 1555 2.31 LINK SG CYS A 28 ZN ZN A 101 1555 1555 2.29 LINK SG CYS A 31 ZN ZN A 101 1555 1555 2.30 SITE 1 AC1 4 CYS A 7 CYS A 10 CYS A 28 CYS A 31 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