HEADER DNA BINDING PROTEIN/DNA 30-JUL-09 2KMK TITLE GFI-1 ZINC FINGERS 3-5 COMPLEXED WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER PROTEIN GFI-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 312-393; COMPND 5 SYNONYM: GROWTH FACTOR INDEPENDENT PROTEIN 1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP*TP*GP*CP*CP*TP*A)- COMPND 9 3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*TP*AP*GP*GP*CP*AP*GP*TP*GP*AP*TP*TP*TP*AP*TP*G)- COMPND 14 3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: GFI1, GFI-1; 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: PET17B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS TANDEM REPEAT ZINC FINGER DOMAIN, PROTEIN-DNA COMPLEX, DNA-BINDING, KEYWDS 2 METAL-BINDING, NUCLEUS, TRANSCRIPTION, TRANSCRIPTION REGULATION, KEYWDS 3 ZINC, ZINC-FINGER, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR S.LEE,Z.WU REVDAT 2 26-MAY-10 2KMK 1 JRNL REVDAT 1 02-MAR-10 2KMK 0 JRNL AUTH S.LEE,K.DODDAPANENI,A.HOGUE,L.MCGHEE,S.MEYERS,Z.WU JRNL TITL SOLUTION STRUCTURE OF GFI-1 ZINC DOMAIN BOUND TO CONSENSUS JRNL TITL 2 DNA. JRNL REF J.MOL.BIOL. V. 397 1055 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20153336 JRNL DOI 10.1016/J.JMB.2010.02.006 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KMK COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-09. REMARK 100 THE RCSB ID CODE IS RCSB101306. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 305 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 25 MM [U-2H] SODIUM ACETATE-1, REMARK 210 0.1 MM ZINC CHLORIDE-2, 0.1 MM REMARK 210 BETA-MERCAPTOETHANOL-3, 0.04 % REMARK 210 SODIUM AZIDE-4, 93% H2O/7% D2O; REMARK 210 25 MM [U-2H] SODIUM ACETATE-5, REMARK 210 0.1 MM ZINC CHLORIDE-6, 0.1 MM REMARK 210 BETA-MERCAPTOETHANOL-7, 0.4 % REMARK 210 SODIUM AZIDE-8, 7.1 % REMARK 210 POLYACRYLAMIDE-9, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 2D 1H-13C REMARK 210 HSQC; 3D 15N-EDITED TOCSY-HSQC; REMARK 210 3D HCCH-TOCSY; 3D 13C-EDITED REMARK 210 NOESY-CTHSQC; 2D 13C,15N-EDITED REMARK 210 TOCSY; 2D 13C,15N-EDITED NOESY; REMARK 210 3D 15N-EDITED 1H-15N NOESY-HSQC; REMARK 210 3D 15N-EDITED 15N-15N NOESY-HSQC; REMARK 210 2D 13C,15N-FILTERED 13C,15N- REMARK 210 SELECTED NOESY; 3D 13C-EDITED REMARK 210 15N,13C-FILTERED NOESY-HSQC; 2D REMARK 210 1H-15N TROSY-ANTITROSY; 3D (HA) REMARK 210 CA(CO)NH; 3D HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRDRAW, NMRVIEW, X- REMARK 210 PLOR_NIH, XWINNMR REMARK 210 METHOD USED : SIMULATED ANNEALING, DISTANCE REMARK 210 GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-12 REMARK 470 RES CSSEQI ATOMS REMARK 470 GLY A 82 O 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 HH21 ARG A 13 H SER A 15 1.41 REMARK 500 O SER A 70 H ILE A 74 1.56 REMARK 500 O LEU A 17 H LEU A 21 1.59 REMARK 500 O HIS A 52 N GLY A 54 2.02 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 11 DT B 103 C5 DT B 103 C7 0.036 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 1 DT B 103 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT B 103 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT C 208 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DT B 103 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 DT C 213 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 4 DT B 103 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DT B 107 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 DT B 103 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 5 DT B 107 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 6 DT B 103 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 7 DT B 103 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 7 DT B 107 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 7 DT C 213 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 8 DT B 103 C4 - C5 - C6 ANGL. DEV. = 3.8 DEGREES REMARK 500 8 DT B 103 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 8 DT C 213 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 9 DT B 103 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 DT B 103 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 9 DT B 107 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 10 DT B 103 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES REMARK 500 10 DT B 103 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 10 DT C 208 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 11 DT B 103 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 11 DT B 107 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 11 DT C 211 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 12 DT B 103 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 12 DT B 103 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES 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 LYS A 5 32.11 -95.33 REMARK 500 1 ILE A 6 -71.17 -126.81 REMARK 500 1 TYR A 34 -76.75 -110.58 REMARK 500 1 LYS A 37 174.95 -54.35 REMARK 500 1 LYS A 42 -72.20 -37.88 REMARK 500 1 THR A 49 -33.04 -38.92 REMARK 500 1 HIS A 52 -103.12 -80.11 REMARK 500 1 THR A 53 -37.03 -8.68 REMARK 500 2 ILE A 6 -72.04 -125.27 REMARK 500 2 ASP A 26 54.63 97.66 REMARK 500 2 ARG A 28 65.83 36.33 REMARK 500 2 TYR A 34 -73.38 -103.95 REMARK 500 2 THR A 49 -38.31 -39.90 REMARK 500 2 CYS A 60 -89.02 -54.41 REMARK 500 2 GLN A 61 -10.17 120.06 REMARK 500 3 ASP A 26 57.42 36.31 REMARK 500 3 TYR A 34 -70.45 -113.86 REMARK 500 3 LYS A 42 -80.59 -30.95 REMARK 500 3 SER A 43 -31.15 -36.12 REMARK 500 4 ILE A 6 -72.75 -77.91 REMARK 500 4 TYR A 34 -73.42 -117.67 REMARK 500 4 LYS A 42 -82.47 -29.74 REMARK 500 4 SER A 43 -30.42 -37.71 REMARK 500 5 ILE A 6 -58.24 -123.72 REMARK 500 5 LYS A 42 -74.21 -34.32 REMARK 500 5 LYS A 56 79.66 -115.49 REMARK 500 6 CYS A 4 157.21 -13.88 REMARK 500 6 ILE A 6 -80.35 -126.13 REMARK 500 6 ASP A 26 59.86 32.47 REMARK 500 6 TYR A 34 -74.29 -104.71 REMARK 500 6 GLN A 41 105.73 179.72 REMARK 500 7 ILE A 6 -70.00 -83.14 REMARK 500 7 ASP A 26 73.22 46.21 REMARK 500 7 TYR A 34 -66.61 -109.77 REMARK 500 7 LYS A 37 154.44 -46.55 REMARK 500 7 CYS A 60 -86.68 -38.47 REMARK 500 7 GLN A 61 -16.51 117.10 REMARK 500 7 VAL A 62 -63.04 -95.86 REMARK 500 8 LYS A 5 32.12 -98.82 REMARK 500 8 ILE A 6 -78.38 -126.92 REMARK 500 8 ASP A 26 51.50 27.88 REMARK 500 8 ARG A 28 65.76 37.33 REMARK 500 8 PRO A 29 31.58 -83.07 REMARK 500 8 TYR A 34 -71.02 -111.89 REMARK 500 8 LYS A 37 149.34 -26.57 REMARK 500 8 LYS A 42 -71.05 -41.98 REMARK 500 8 LYS A 56 70.75 -117.86 REMARK 500 9 CYS A 7 -27.75 -142.07 REMARK 500 9 TYR A 34 -69.78 -102.91 REMARK 500 9 LYS A 37 156.91 -47.14 REMARK 500 REMARK 500 THIS ENTRY HAS 64 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 1 ZN A 83 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 4 SG REMARK 620 2 CYS A 7 SG 110.4 REMARK 620 3 HIS A 20 NE2 109.2 108.2 REMARK 620 4 HIS A 24 NE2 109.4 115.4 104.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 84 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 32 SG REMARK 620 2 CYS A 35 SG 110.5 REMARK 620 3 HIS A 48 NE2 108.0 108.6 REMARK 620 4 HIS A 52 NE2 110.3 114.6 104.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 85 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 60 SG REMARK 620 2 CYS A 63 SG 109.6 REMARK 620 3 HIS A 76 NE2 113.3 109.9 REMARK 620 4 HIS A 80 NE2 109.6 112.3 102.0 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 83 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 84 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 85 DBREF 2KMK A 1 82 UNP Q07120 GFI1_RAT 312 393 DBREF 2KMK B 101 116 PDB 2KMK 2KMK 101 116 DBREF 2KMK C 201 216 PDB 2KMK 2KMK 201 216 SEQRES 1 A 82 SER PHE ASP CYS LYS ILE CYS GLY LYS SER PHE LYS ARG SEQRES 2 A 82 SER SER THR LEU SER THR HIS LEU LEU ILE HIS SER ASP SEQRES 3 A 82 THR ARG PRO TYR PRO CYS GLN TYR CYS GLY LYS ARG PHE SEQRES 4 A 82 HIS GLN LYS SER ASP MET LYS LYS HIS THR PHE ILE HIS SEQRES 5 A 82 THR GLY GLU LYS PRO HIS LYS CYS GLN VAL CYS GLY LYS SEQRES 6 A 82 ALA PHE SER GLN SER SER ASN LEU ILE THR HIS SER ARG SEQRES 7 A 82 LYS HIS THR GLY SEQRES 1 B 16 DC DA DT DA DA DA DT DC DA DC DT DG DC SEQRES 2 B 16 DC DT DA SEQRES 1 C 16 DT DA DG DG DC DA DG DT DG DA DT DT DT SEQRES 2 C 16 DA DT DG HET ZN A 83 1 HET ZN A 84 1 HET ZN A 85 1 HETNAM ZN ZINC ION FORMUL 4 ZN 3(ZN 2+) HELIX 1 1 ARG A 13 ASP A 26 1 14 HELIX 2 2 GLN A 41 GLY A 54 1 14 HELIX 3 3 GLN A 69 GLY A 82 1 14 SHEET 1 A 2 PHE A 2 ASP A 3 0 SHEET 2 A 2 SER A 10 PHE A 11 -1 O PHE A 11 N PHE A 2 SHEET 1 B 2 TYR A 30 PRO A 31 0 SHEET 2 B 2 ARG A 38 PHE A 39 -1 O PHE A 39 N TYR A 30 SHEET 1 C 2 HIS A 58 LYS A 59 0 SHEET 2 C 2 ALA A 66 PHE A 67 -1 O PHE A 67 N HIS A 58 LINK SG CYS A 4 ZN ZN A 83 1555 1555 2.27 LINK SG CYS A 7 ZN ZN A 83 1555 1555 2.30 LINK NE2 HIS A 20 ZN ZN A 83 1555 1555 1.94 LINK NE2 HIS A 24 ZN ZN A 83 1555 1555 1.99 LINK SG CYS A 32 ZN ZN A 84 1555 1555 2.28 LINK SG CYS A 35 ZN ZN A 84 1555 1555 2.29 LINK NE2 HIS A 48 ZN ZN A 84 1555 1555 1.94 LINK NE2 HIS A 52 ZN ZN A 84 1555 1555 1.98 LINK SG CYS A 60 ZN ZN A 85 1555 1555 2.32 LINK SG CYS A 63 ZN ZN A 85 1555 1555 2.30 LINK NE2 HIS A 76 ZN ZN A 85 1555 1555 1.96 LINK NE2 HIS A 80 ZN ZN A 85 1555 1555 1.98 SITE 1 AC1 4 CYS A 4 CYS A 7 HIS A 20 HIS A 24 SITE 1 AC2 4 CYS A 32 CYS A 35 HIS A 48 HIS A 52 SITE 1 AC3 4 CYS A 60 CYS A 63 HIS A 76 HIS A 80 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 263 0 3 3 6 0 3 6 0 0 0 11 END