PDB Short entry for 2KKT HEADER TRANSCRIPTION 29-JUN-09 2KKT TITLE SOLUTION STRUCTURE OF THE SCA7 DOMAIN OF HUMAN ATAXIN-7-L3 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATAXIN-7-LIKE PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SCA7 DOMAIN; COMPND 5 SYNONYM: SAGA-ASSOCIATED FACTOR 11 HOMOLOG; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ATXN7L3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PGEX-4T1 KEYWDS ZINC FINGER, TRANSCRIPTION, ACTIVATOR, ALTERNATIVE SPLICING, KEYWDS 2 CHROMATIN REGULATOR, METAL-BINDING, NUCLEUS, PHOSPHOPROTEIN, KEYWDS 3 TRANSCRIPTION REGULATION, ZINC, ZINC-FINGER EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.WANG,A.R.ATKINSON,J.BONNET,C.ROMIER,B.KIEFFER REVDAT 2 16-MAR-22 2KKT 1 REMARK SEQADV REVDAT 1 16-JUN-10 2KKT 0 JRNL AUTH J.BONNET,Y.WANG,A.ATKINSON,J.KOFFLER,C.ROMIER,A.HAMICHE, JRNL AUTH 2 L.TORA,D.DEVYS,B.KIEFFER JRNL TITL HISTONE DEUBIQUITINATION BY SAGA IS MODULATED BY AN ATYPICAL JRNL TITL 2 ZINC FINGER DOMAIN OF ATAXIN-7 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IN EXPLICIT WATER USING RECOORD REMARK 3 PROTOCOL REMARK 4 REMARK 4 2KKT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000101244. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 7.1 REMARK 210 IONIC STRENGTH : 0.3 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 50MM SODIUM PHOSPHATE-1, 200MM REMARK 210 SODIUM CHLORIDE-2, 2MM DTT-3, REMARK 210 0.15MM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN-4, 90% H2O/10% D2O; 50MM REMARK 210 SODIUM PHOSPHATE-5, 200MM SODIUM REMARK 210 CHLORIDE-6, 2MM DTT-7, 0.6MM REMARK 210 PROTEIN-8, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D HCCH-TOCSY; 2D 1H- REMARK 210 1H NOESY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 64 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 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 193 REMARK 465 SER A 194 REMARK 465 HIS A 195 REMARK 465 MET A 196 REMARK 465 GLY A 197 REMARK 465 GLU A 250 REMARK 465 VAL A 251 REMARK 465 GLU A 252 REMARK 465 SER A 253 REMARK 465 SER A 254 REMARK 465 LEU A 255 REMARK 465 ASP A 256 REMARK 465 ASN A 257 REMARK 465 ASP A 258 REMARK 465 SER A 259 REMARK 465 PHE A 260 REMARK 465 ASP A 261 REMARK 465 MET A 262 REMARK 465 THR A 263 REMARK 465 ASP A 264 REMARK 465 SER A 265 REMARK 465 GLN A 266 REMARK 465 ALA A 267 REMARK 465 LEU A 268 REMARK 465 ILE A 269 REMARK 465 SER A 270 REMARK 465 ARG A 271 REMARK 465 LEU A 272 REMARK 465 GLN A 273 REMARK 465 TRP A 274 REMARK 465 ASP A 275 REMARK 465 GLY A 276 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 2 HIS A 229 CB HIS A 229 CG 0.110 REMARK 500 2 HIS A 229 CG HIS A 229 ND1 0.158 REMARK 500 2 ARG A 234 NE ARG A 234 CZ -0.135 REMARK 500 4 PRO A 227 CD PRO A 227 N -0.090 REMARK 500 6 HIS A 229 CB HIS A 229 CG 0.108 REMARK 500 6 HIS A 229 CG HIS A 229 ND1 0.137 REMARK 500 9 HIS A 229 CG HIS A 229 ND1 0.167 REMARK 500 12 HIS A 229 CG HIS A 229 ND1 0.132 REMARK 500 17 PRO A 227 CD PRO A 227 N -0.094 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 PRO A 227 N - CA - CB ANGL. DEV. = -7.8 DEGREES REMARK 500 2 PRO A 227 N - CA - CB ANGL. DEV. = -8.6 DEGREES REMARK 500 3 CYS A 226 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 4 CYS A 226 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 5 PRO A 227 N - CA - CB ANGL. DEV. = -7.7 DEGREES REMARK 500 7 CYS A 226 CA - CB - SG ANGL. DEV. = 6.6 DEGREES REMARK 500 9 PRO A 227 N - CA - CB ANGL. DEV. = -9.8 DEGREES REMARK 500 13 CYS A 226 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 14 CYS A 226 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 17 CYS A 226 CA - CB - SG ANGL. DEV. = 7.6 DEGREES REMARK 500 18 CYS A 226 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 19 CYS A 226 CA - CB - SG ANGL. DEV. = 6.8 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 HIS A 215 -52.94 65.85 REMARK 500 1 LYS A 218 -173.72 77.16 REMARK 500 1 PRO A 227 -114.83 -127.44 REMARK 500 1 ALA A 246 40.13 -99.83 REMARK 500 2 THR A 207 -24.45 -141.46 REMARK 500 2 SER A 213 -78.15 -42.67 REMARK 500 2 GLU A 214 72.42 -157.29 REMARK 500 2 HIS A 215 -40.29 55.89 REMARK 500 2 LYS A 218 -164.28 -115.16 REMARK 500 2 ARG A 222 -169.57 -77.18 REMARK 500 2 PRO A 227 -114.74 -130.51 REMARK 500 2 ALA A 246 32.16 -91.16 REMARK 500 3 CYS A 209 -78.85 -42.45 REMARK 500 3 GLU A 214 24.15 46.92 REMARK 500 3 LYS A 217 -89.08 -87.93 REMARK 500 3 LYS A 218 -158.78 170.98 REMARK 500 3 PRO A 227 -93.45 -118.22 REMARK 500 3 ALA A 246 37.16 -80.55 REMARK 500 3 LEU A 248 149.09 67.12 REMARK 500 4 LEU A 205 -7.74 -57.22 REMARK 500 4 CYS A 209 -76.36 -39.37 REMARK 500 4 GLU A 214 88.73 -175.22 REMARK 500 4 HIS A 215 -76.37 48.48 REMARK 500 4 LYS A 218 -169.02 -64.39 REMARK 500 4 ARG A 222 -168.38 -69.83 REMARK 500 4 CYS A 226 -65.96 -18.40 REMARK 500 4 PRO A 227 -80.29 -106.73 REMARK 500 4 GLN A 228 33.19 -142.18 REMARK 500 5 THR A 207 -2.05 -140.72 REMARK 500 5 GLU A 214 12.21 59.14 REMARK 500 5 HIS A 215 -29.10 70.13 REMARK 500 5 LYS A 217 -92.99 -90.31 REMARK 500 5 LYS A 218 -165.82 -178.25 REMARK 500 5 PRO A 227 -109.93 -125.98 REMARK 500 5 VAL A 247 79.77 -102.42 REMARK 500 6 CYS A 209 -77.78 -47.24 REMARK 500 6 LYS A 218 -159.08 72.89 REMARK 500 6 CYS A 226 -63.09 -22.26 REMARK 500 6 PRO A 227 -92.89 -115.58 REMARK 500 7 THR A 207 -15.61 -140.29 REMARK 500 7 CYS A 209 -79.58 -45.60 REMARK 500 7 GLU A 214 167.77 179.63 REMARK 500 7 LYS A 217 -152.49 -123.94 REMARK 500 7 LYS A 218 -157.88 -142.27 REMARK 500 7 PRO A 227 -98.41 -119.51 REMARK 500 8 GLU A 214 -75.73 67.32 REMARK 500 8 THR A 216 -39.59 78.22 REMARK 500 8 LYS A 218 -170.72 54.71 REMARK 500 8 ARG A 222 -170.76 -66.86 REMARK 500 8 PRO A 227 -106.41 -124.23 REMARK 500 REMARK 500 THIS ENTRY HAS 138 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 ARG A 235 0.07 SIDE CHAIN REMARK 500 3 ARG A 234 0.10 SIDE CHAIN REMARK 500 4 ARG A 234 0.16 SIDE CHAIN REMARK 500 5 ARG A 234 0.14 SIDE CHAIN REMARK 500 6 ARG A 234 0.12 SIDE CHAIN REMARK 500 7 ARG A 234 0.09 SIDE CHAIN REMARK 500 10 ARG A 234 0.17 SIDE CHAIN REMARK 500 11 ARG A 234 0.15 SIDE CHAIN REMARK 500 12 ARG A 234 0.09 SIDE CHAIN REMARK 500 14 ARG A 234 0.17 SIDE CHAIN REMARK 500 15 ARG A 234 0.13 SIDE CHAIN REMARK 500 16 ARG A 234 0.16 SIDE CHAIN REMARK 500 17 ARG A 234 0.12 SIDE CHAIN REMARK 500 18 ARG A 234 0.10 SIDE CHAIN REMARK 500 19 ARG A 234 0.15 SIDE CHAIN REMARK 500 20 ARG A 234 0.18 SIDE CHAIN REMARK 500 20 ARG A 235 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 500 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 209 SG REMARK 620 2 CYS A 220 SG 105.6 REMARK 620 3 CYS A 226 SG 108.6 106.0 REMARK 620 4 HIS A 229 ND1 103.6 112.0 120.2 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 500 DBREF 2KKT A 197 276 UNP Q14CW9 AT7L3_HUMAN 197 276 SEQADV 2KKT GLY A 193 UNP Q14CW9 EXPRESSION TAG SEQADV 2KKT SER A 194 UNP Q14CW9 EXPRESSION TAG SEQADV 2KKT HIS A 195 UNP Q14CW9 EXPRESSION TAG SEQADV 2KKT MET A 196 UNP Q14CW9 EXPRESSION TAG SEQADV 2KKT VAL A 239 UNP Q14CW9 ILE 239 ENGINEERED MUTATION SEQRES 1 A 84 GLY SER HIS MET GLY PRO GLU GLU LEU ARG SER LEU LEU SEQRES 2 A 84 THR THR GLN CYS GLY VAL ILE SER GLU HIS THR LYS LYS SEQRES 3 A 84 MET CYS THR ARG SER LEU ARG CYS PRO GLN HIS THR ASP SEQRES 4 A 84 GLU GLN ARG ARG THR VAL ARG VAL TYR PHE LEU GLY PRO SEQRES 5 A 84 SER ALA VAL LEU PRO GLU VAL GLU SER SER LEU ASP ASN SEQRES 6 A 84 ASP SER PHE ASP MET THR ASP SER GLN ALA LEU ILE SER SEQRES 7 A 84 ARG LEU GLN TRP ASP GLY HET ZN A 500 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 PRO A 198 LEU A 205 1 8 HELIX 2 2 THR A 230 LEU A 242 1 13 LINK SG CYS A 209 ZN ZN A 500 1555 1555 2.32 LINK SG CYS A 220 ZN ZN A 500 1555 1555 2.30 LINK SG CYS A 226 ZN ZN A 500 1555 1555 2.38 LINK ND1 HIS A 229 ZN ZN A 500 1555 1555 2.21 SITE 1 AC1 6 CYS A 209 VAL A 211 CYS A 220 CYS A 226 SITE 2 AC1 6 PRO A 227 HIS A 229 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