Header list of 1y0j.pdb file
Complete list - r 2 2 Bytes
HEADER DNA BINDING PROTEIN 15-NOV-04 1Y0J TITLE ZINC FINGERS AS PROTEIN RECOGNITION MOTIFS: STRUCTURAL BASIS FOR THE TITLE 2 GATA-1/FRIEND OF GATA INTERACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ERYTHROID TRANSCRIPTION FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GNF; COMPND 5 SYNONYM: GATA-1, ERYF1, GF-1, NF-E1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ZINC-FINGER PROTEIN USH; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: USF1; COMPND 11 SYNONYM: U-SHAPED TRANSCRIPTION FACTOR, U-SHAPED PROTEIN; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: GATA-1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-2T; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 13 ORGANISM_COMMON: FRUIT FLY; SOURCE 14 ORGANISM_TAXID: 7227; SOURCE 15 GENE: U-SHAPED; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS ZINC FINGER, GATA-1, FOG, PROTEIN-PROTEIN COMPLEX, DNA BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.K.LIEW,R.J.Y.SIMPSON,A.H.Y.KWAN,L.A.CROFTS,F.E.LOUGHLIN, AUTHOR 2 J.M.MATTHEWS,M.CROSSLEY,J.P.MACKAY REVDAT 3 02-MAR-22 1Y0J 1 REMARK SEQADV REVDAT 2 24-FEB-09 1Y0J 1 VERSN REVDAT 1 25-JAN-05 1Y0J 0 JRNL AUTH C.K.LIEW,R.J.Y.SIMPSON,A.H.Y.KWAN,L.A.CROFTS,F.E.LOUGHLIN, JRNL AUTH 2 J.M.MATTHEWS,M.CROSSLEY,J.P.MACKAY JRNL TITL ZINC FINGERS AS PROTEIN RECOGNITION MOTIFS: STRUCTURAL BASIS JRNL TITL 2 FOR THE GATA-1/FRIEND OF GATA INTERACTION JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 583 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15644435 JRNL DOI 10.1073/PNAS.0407511102 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.5, HADDOCK 1.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), DONMINGUEZ ET AL (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STANDARD TRIPLE-RESONANCE NMR REMARK 3 SPECTROSCOPY WAS FIRST USED TO DETERMINE THE PRELIMINARY REMARK 3 STRUCTURE OF THE COMPLEX. SINCE THE BACKBONE FOLDS OF BOTH GNF REMARK 3 AND USF1 DID NOT APPEAR TO BE SUBSTANTIALLY ALTERED TO THOSE OF REMARK 3 THE PROTEINS IN ISOLATION, THE COMPUTER PROGRAM HADDOCK WAS USED REMARK 3 TO DOCK THE TWO PARTNER PROTEINS USING INTERMOLECULAR NOES REMARK 3 OBTAINED FROM DOUBLE HALF-FILTERED NOESY EXPERIMENTS, AND REMARK 3 AMBIGUOUS RESTRAINTS DERIVED FROM MUTAGENESIS AND NMR TITRATION REMARK 3 EXPERIMENTS. REMARK 4 REMARK 4 1Y0J COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030962. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 280 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM GNF U-15N,13C; 2MM TRIS REMARK 210 -CARBOXYETHYLPHOSPHINE (TCEP); REMARK 210 1MM ZINC SULPHATE; 20MM SODIUM REMARK 210 ACETATE; 0.5MM GNF U-15N,13C; REMARK 210 0.6MM USF1; 2MM TRIS- REMARK 210 CARBOXYETHYLPHOSPHINE (TCEP); REMARK 210 1MM ZINC SULPHATE; 20MM SODIUM REMARK 210 ACETATE; 0.5MM USF1 U-15N,13C; REMARK 210 2MM TRIS-CARBOXYETHYLPHOSPHINE REMARK 210 (TCEP); 1MM ZINC SULPHATE; 20MM REMARK 210 SODIUM ACETATE; 0.5MM GNF; 0.6MM REMARK 210 USF1 U-15N,13C; 2MM TRIS- REMARK 210 CARBOXYETHYLPHOSPHINE (TCEP); REMARK 210 1MM ZINC SULPHATE; 20MM SODIUM REMARK 210 ACETATE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCO; HNCA; HNCOCA; CBCA(CO)NH; REMARK 210 15N, 13C DOUBLE DECOUPLED NOESY; REMARK 210 HCCH-TOCSY; 15N, 13C DOUBLE HALF- REMARK 210 FILTERED NOESY; HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1.3.13, ARIA 1.2, HADDOCK REMARK 210 1.0 REMARK 210 METHOD USED : SIMULATED ANNEALING MOLECULAR REMARK 210 DYNAMICS TORSION ANGLE DYNAMICS 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: OTHER COMMONLY USED STANDARD TRIPLE-RESONANCE NMR REMARK 210 EXPERIMENTS WERE ALSO RECORDED. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 198 REMARK 465 SER A 199 REMARK 465 ARG A 239 REMARK 465 PRO A 240 REMARK 465 LEU A 241 REMARK 465 ILE A 242 REMARK 465 ARG A 243 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: 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 211 42.05 -90.74 REMARK 500 1 CYS A 225 -159.94 -89.59 REMARK 500 1 ALA A 227 -63.07 -99.10 REMARK 500 1 SER B 2 -134.24 57.46 REMARK 500 1 LEU B 4 -65.73 68.82 REMARK 500 1 TYR B 30 -62.71 -141.14 REMARK 500 1 CYS B 32 46.30 -82.50 REMARK 500 1 SER B 33 156.79 78.23 REMARK 500 2 ASN A 206 -86.42 -113.64 REMARK 500 2 CYS A 225 -156.60 -94.53 REMARK 500 2 SER B 2 -25.37 71.58 REMARK 500 2 SER B 19 -24.45 -140.39 REMARK 500 2 PRO B 21 46.98 -76.97 REMARK 500 2 SER B 22 20.34 -149.20 REMARK 500 2 GLN B 28 49.68 -78.85 REMARK 500 2 ALA B 29 -36.99 -158.08 REMARK 500 2 SER B 33 -84.92 69.00 REMARK 500 3 CYS A 207 -58.81 -124.26 REMARK 500 3 PHE B 9 52.43 -118.44 REMARK 500 3 TYR B 30 -46.21 -133.99 REMARK 500 3 SER B 33 139.71 76.76 REMARK 500 4 ALA A 201 -81.12 -137.09 REMARK 500 4 ASN A 206 -36.25 -139.64 REMARK 500 4 CYS A 225 -78.69 -58.56 REMARK 500 4 ASN A 226 -45.92 -172.67 REMARK 500 4 SER B 2 -175.76 62.88 REMARK 500 4 LEU B 4 -58.64 72.09 REMARK 500 4 TYR B 30 -50.60 -123.26 REMARK 500 4 SER B 33 85.75 61.57 REMARK 500 5 CYS A 225 -83.17 -61.91 REMARK 500 5 ASN A 226 -45.39 -164.28 REMARK 500 5 SER B 2 -61.19 71.75 REMARK 500 5 ALA B 17 98.84 -67.01 REMARK 500 5 SER B 19 -23.33 -142.54 REMARK 500 5 TYR B 30 -46.58 -136.84 REMARK 500 5 TYR B 31 -73.67 -75.69 REMARK 500 5 SER B 33 179.39 72.07 REMARK 500 6 ASN A 206 -36.05 -132.63 REMARK 500 6 THR A 210 10.03 -145.82 REMARK 500 6 ASP A 218 -157.45 -121.24 REMARK 500 6 CYS A 225 -92.08 -69.51 REMARK 500 6 ASN A 226 -45.00 -151.28 REMARK 500 6 SER B 2 -60.10 70.17 REMARK 500 6 LEU B 3 -97.26 -150.12 REMARK 500 6 SER B 19 -28.34 -141.73 REMARK 500 6 ALA B 29 -41.16 -162.83 REMARK 500 6 SER B 33 -102.27 68.35 REMARK 500 6 HIS B 34 135.92 -170.06 REMARK 500 7 ASP A 218 -144.64 -91.84 REMARK 500 7 CYS A 225 -79.18 -63.39 REMARK 500 REMARK 500 THIS ENTRY HAS 166 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 244 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 204 SG REMARK 620 2 CYS A 207 SG 97.0 REMARK 620 3 CYS A 225 SG 135.5 126.7 REMARK 620 4 CYS A 228 SG 94.8 93.2 91.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 37 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 11 SG REMARK 620 2 CYS B 14 SG 99.6 REMARK 620 3 HIS B 27 NE2 111.8 120.5 REMARK 620 4 CYS B 32 SG 99.8 104.7 117.2 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 244 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 37 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GNF RELATED DB: PDB REMARK 900 STRUCTURE OF ONE COMPONENT (GATA-1 N-FINGER, GNF) OF THE COMPLEX REMARK 900 FROM WHICH THE COMPLEX STRUCTURE IS BASED. REMARK 900 RELATED ID: 1FV5 RELATED DB: PDB REMARK 900 STRUCTURE OF ONE COMPONENT (1ST ZINC FINGER OF U-SHAPED, USF1) OF REMARK 900 THE COMPLEX FROM WHICH THE COMPLEX STRUCTURE IS BASED. DBREF 1Y0J A 200 243 UNP P17679 GATA1_MOUSE 200 243 DBREF 1Y0J B 3 36 UNP Q9VPQ6 USH_DROME 202 235 SEQADV 1Y0J GLY A 198 UNP P17679 EXPRESSION TAG SEQADV 1Y0J SER A 199 UNP P17679 EXPRESSION TAG SEQADV 1Y0J GLY B 1 UNP Q9VPQ6 EXPRESSION TAG SEQADV 1Y0J SER B 2 UNP Q9VPQ6 EXPRESSION TAG SEQRES 1 A 46 GLY SER GLU ALA ARG GLU CYS VAL ASN CYS GLY ALA THR SEQRES 2 A 46 ALA THR PRO LEU TRP ARG ARG ASP ARG THR GLY HIS TYR SEQRES 3 A 46 LEU CYS ASN ALA CYS GLY LEU TYR HIS LYS MET ASN GLY SEQRES 4 A 46 GLN ASN ARG PRO LEU ILE ARG SEQRES 1 B 36 GLY SER LEU LEU LYS PRO ALA ARG PHE MET CYS LEU PRO SEQRES 2 B 36 CYS GLY ILE ALA PHE SER SER PRO SER THR LEU GLU ALA SEQRES 3 B 36 HIS GLN ALA TYR TYR CYS SER HIS ARG ILE HET ZN A 244 1 HET ZN B 37 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) HELIX 1 1 ALA A 227 ASN A 235 1 9 HELIX 2 2 SER B 20 GLN B 28 1 9 SHEET 1 A 2 ARG A 216 ARG A 217 0 SHEET 2 A 2 TYR A 223 LEU A 224 -1 O LEU A 224 N ARG A 216 LINK SG CYS A 204 ZN ZN A 244 1555 1555 2.27 LINK SG CYS A 207 ZN ZN A 244 1555 1555 2.30 LINK SG CYS A 225 ZN ZN A 244 1555 1555 2.25 LINK SG CYS A 228 ZN ZN A 244 1555 1555 2.35 LINK SG CYS B 11 ZN ZN B 37 1555 1555 2.29 LINK SG CYS B 14 ZN ZN B 37 1555 1555 2.26 LINK NE2 HIS B 27 ZN ZN B 37 1555 1555 1.91 LINK SG CYS B 32 ZN ZN B 37 1555 1555 2.28 SITE 1 AC1 4 CYS A 204 CYS A 207 CYS A 225 CYS A 228 SITE 1 AC2 4 CYS B 11 CYS B 14 HIS B 27 CYS B 32 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 MODEL 1
Complete list - r 2 2 Bytes