PDB Short entry for 2JM1 HEADER METAL BINDING PROTEIN 13-SEP-06 2JM1 TITLE STRUCTURES AND CHEMICAL SHIFT ASSIGNMENTS FOR THE ADD DOMAIN OF THE TITLE 2 ATRX PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR ATRX; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ADD DOMAIN, RESIDUES 159-296; COMPND 5 SYNONYM: ATP-DEPENDENT HELICASE ATRX, X-LINKED HELICASE II, X-LINKED COMPND 6 NUCLEAR PROTEIN, XNP, ZNF- HX; COMPND 7 EC: 3.6.1.-; COMPND 8 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: ATRX, RAD54L, XH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 ROSETTA PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS ADD DOMAIN, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 32 AUTHOR J.YANG,D.NEUHAUS REVDAT 5 20-DEC-23 2JM1 1 REMARK REVDAT 4 09-MAR-22 2JM1 1 REMARK SEQADV REVDAT 3 23-JUN-10 2JM1 1 JRNL REVDAT 2 24-FEB-09 2JM1 1 VERSN REVDAT 1 26-JUN-07 2JM1 0 JRNL AUTH A.ARGENTARO,J.C.YANG,L.CHAPMAN,M.S.KOWALCZYK,R.J.GIBBONS, JRNL AUTH 2 D.R.HIGGS,D.NEUHAUS,D.RHODES JRNL TITL STRUCTURAL CONSEQUENCES OF DISEASE-CAUSING MUTATIONS IN THE JRNL TITL 2 ATRX-DNMT3-DNMT3L (ADD) DOMAIN OF THE CHROMATIN-ASSOCIATED JRNL TITL 3 PROTEIN ATRX. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 11939 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17609377 JRNL DOI 10.1073/PNAS.0704057104 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, X-PLOR 3.8 REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), AT BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JM1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000100001. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 0.5 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7 MM [U-15N] ADD DOMAIN 156 REMARK 210 -296, 20 MM TRIS, 1 MM DTT, 100 REMARK 210 UM ZINC CHLORIDE, 0.5 M SODIUM REMARK 210 CHLORIDE, 93% H2O, 7% D2O; 0.35 REMARK 210 MM [U-13C; U-15N] ADD DOMAIN 156- REMARK 210 296, 20 MM TRIS, 1 MM DTT, 100 REMARK 210 UM ZINC CHLORIDE, 0.5 M SODIUM REMARK 210 CHLORIDE, 93% H2O, 7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D NOESY; 3D 1H REMARK 210 -15N NOESY; 3D HNHB; 2D 1H-13C REMARK 210 HSQC; 3D HNCACB; 3D HN(COCA)CB; REMARK 210 3D HN(CO)CA; HNHAHB; HN(CO)HAHB; REMARK 210 3D HCCH-TOCSY; 3D HCCH-COSY; 3D REMARK 210 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, SPARKY, X-PLOR 3.8 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 32 REMARK 210 CONFORMERS, SELECTION CRITERIA : 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 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: 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 ASN A 179 95.06 -51.13 REMARK 500 1 HIS A 180 -175.58 51.31 REMARK 500 1 SER A 185 -69.07 -94.93 REMARK 500 1 ILE A 186 157.27 -49.66 REMARK 500 1 SER A 210 110.89 -169.15 REMARK 500 1 ARG A 211 81.19 51.55 REMARK 500 1 SER A 213 -71.15 64.33 REMARK 500 1 GLU A 218 51.74 -144.09 REMARK 500 1 TRP A 222 -59.95 -149.84 REMARK 500 1 GLU A 225 -169.77 -123.55 REMARK 500 1 ASN A 228 91.95 52.06 REMARK 500 1 PHE A 234 -60.11 -147.67 REMARK 500 1 LEU A 248 26.58 -148.35 REMARK 500 1 ASP A 258 69.54 -170.04 REMARK 500 1 GLU A 259 -67.28 -131.62 REMARK 500 1 ASN A 260 40.75 -146.29 REMARK 500 1 GLN A 262 111.84 -170.71 REMARK 500 1 CYS A 265 -147.36 -141.72 REMARK 500 1 LEU A 273 31.55 -147.93 REMARK 500 2 MET A 158 -60.04 -142.40 REMARK 500 2 LEU A 165 87.94 52.81 REMARK 500 2 ASN A 179 93.78 -52.63 REMARK 500 2 HIS A 180 -174.74 50.71 REMARK 500 2 SER A 185 -69.35 -93.23 REMARK 500 2 SER A 210 -167.49 -112.45 REMARK 500 2 ASP A 212 178.55 -53.40 REMARK 500 2 ASP A 214 30.90 -98.47 REMARK 500 2 TRP A 222 -60.39 -149.94 REMARK 500 2 ASP A 233 40.57 -107.30 REMARK 500 2 PHE A 234 -58.67 -151.03 REMARK 500 2 LEU A 248 25.02 -145.93 REMARK 500 2 ASP A 258 61.06 -170.86 REMARK 500 2 GLU A 259 -65.69 -128.59 REMARK 500 2 ASN A 260 36.13 -152.33 REMARK 500 2 CYS A 265 -148.52 -123.26 REMARK 500 2 PRO A 270 74.03 -68.65 REMARK 500 2 LEU A 273 35.09 -155.60 REMARK 500 2 GLN A 293 46.91 -101.68 REMARK 500 2 ASN A 294 82.70 -153.47 REMARK 500 3 ASN A 179 94.03 -52.94 REMARK 500 3 HIS A 180 -173.84 51.45 REMARK 500 3 SER A 185 -69.12 -92.58 REMARK 500 3 SER A 210 108.98 -170.37 REMARK 500 3 ARG A 211 77.56 52.48 REMARK 500 3 SER A 213 -74.73 61.24 REMARK 500 3 GLU A 218 52.78 -145.97 REMARK 500 3 TRP A 222 -60.59 -149.79 REMARK 500 3 GLU A 225 -169.01 -117.81 REMARK 500 3 PHE A 234 -60.79 -150.06 REMARK 500 3 LEU A 248 24.59 -145.32 REMARK 500 REMARK 500 THIS ENTRY HAS 611 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 1 ARG A 160 0.24 SIDE CHAIN REMARK 500 1 ARG A 188 0.28 SIDE CHAIN REMARK 500 1 ARG A 211 0.31 SIDE CHAIN REMARK 500 1 ARG A 221 0.27 SIDE CHAIN REMARK 500 1 ARG A 246 0.30 SIDE CHAIN REMARK 500 1 ARG A 250 0.32 SIDE CHAIN REMARK 500 2 ARG A 160 0.31 SIDE CHAIN REMARK 500 2 ARG A 188 0.32 SIDE CHAIN REMARK 500 2 ARG A 211 0.26 SIDE CHAIN REMARK 500 2 ARG A 221 0.22 SIDE CHAIN REMARK 500 2 ARG A 246 0.31 SIDE CHAIN REMARK 500 2 ARG A 250 0.32 SIDE CHAIN REMARK 500 3 ARG A 160 0.26 SIDE CHAIN REMARK 500 3 ARG A 188 0.26 SIDE CHAIN REMARK 500 3 ARG A 211 0.29 SIDE CHAIN REMARK 500 3 ARG A 221 0.21 SIDE CHAIN REMARK 500 3 ARG A 246 0.28 SIDE CHAIN REMARK 500 3 ARG A 250 0.30 SIDE CHAIN REMARK 500 4 ARG A 160 0.24 SIDE CHAIN REMARK 500 4 ARG A 188 0.31 SIDE CHAIN REMARK 500 4 ARG A 211 0.27 SIDE CHAIN REMARK 500 4 ARG A 221 0.30 SIDE CHAIN REMARK 500 4 ARG A 246 0.29 SIDE CHAIN REMARK 500 4 ARG A 250 0.30 SIDE CHAIN REMARK 500 5 ARG A 160 0.28 SIDE CHAIN REMARK 500 5 ARG A 188 0.24 SIDE CHAIN REMARK 500 5 ARG A 211 0.21 SIDE CHAIN REMARK 500 5 ARG A 221 0.29 SIDE CHAIN REMARK 500 5 ARG A 246 0.30 SIDE CHAIN REMARK 500 5 ARG A 250 0.21 SIDE CHAIN REMARK 500 6 ARG A 160 0.32 SIDE CHAIN REMARK 500 6 ARG A 188 0.24 SIDE CHAIN REMARK 500 6 ARG A 211 0.23 SIDE CHAIN REMARK 500 6 ARG A 221 0.27 SIDE CHAIN REMARK 500 6 ARG A 246 0.24 SIDE CHAIN REMARK 500 6 ARG A 250 0.27 SIDE CHAIN REMARK 500 7 ARG A 160 0.32 SIDE CHAIN REMARK 500 7 ARG A 188 0.22 SIDE CHAIN REMARK 500 7 ARG A 211 0.28 SIDE CHAIN REMARK 500 7 ARG A 221 0.31 SIDE CHAIN REMARK 500 7 ARG A 246 0.30 SIDE CHAIN REMARK 500 7 ARG A 250 0.31 SIDE CHAIN REMARK 500 8 ARG A 160 0.25 SIDE CHAIN REMARK 500 8 ARG A 188 0.28 SIDE CHAIN REMARK 500 8 ARG A 211 0.26 SIDE CHAIN REMARK 500 8 ARG A 221 0.29 SIDE CHAIN REMARK 500 8 ARG A 246 0.32 SIDE CHAIN REMARK 500 8 ARG A 250 0.24 SIDE CHAIN REMARK 500 9 ARG A 160 0.32 SIDE CHAIN REMARK 500 9 ARG A 188 0.31 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 192 PLANE DEVIATIONS. 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 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 171 SG REMARK 620 2 CYS A 174 SG 112.6 REMARK 620 3 CYS A 197 SG 111.6 110.2 REMARK 620 4 CYS A 200 SG 110.0 103.2 108.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 220 SG REMARK 620 2 CYS A 223 SG 107.1 REMARK 620 3 CYS A 240 SG 107.1 109.9 REMARK 620 4 CYS A 243 SG 111.6 114.3 106.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 3 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 232 SG REMARK 620 2 CYS A 235 SG 112.2 REMARK 620 3 CYS A 265 SG 107.8 104.5 REMARK 620 4 CYS A 268 SG 110.2 105.3 116.8 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15001 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT ASSIGNMENTS DBREF 2JM1 A 156 296 UNP P46100 ATRX_HUMAN 159 296 SEQADV 2JM1 GLY A 156 UNP P46100 CLONING ARTIFACT SEQADV 2JM1 ALA A 157 UNP P46100 CLONING ARTIFACT SEQADV 2JM1 MET A 158 UNP P46100 CLONING ARTIFACT SEQRES 1 A 141 GLY ALA MET LYS ARG GLY GLU ASP GLY LEU HIS GLY ILE SEQRES 2 A 141 VAL SER CYS THR ALA CYS GLY GLN GLN VAL ASN HIS PHE SEQRES 3 A 141 GLN LYS ASP SER ILE TYR ARG HIS PRO SER LEU GLN VAL SEQRES 4 A 141 LEU ILE CYS LYS ASN CYS PHE LYS TYR TYR MET SER ASP SEQRES 5 A 141 ASP ILE SER ARG ASP SER ASP GLY MET ASP GLU GLN CYS SEQRES 6 A 141 ARG TRP CYS ALA GLU GLY GLY ASN LEU ILE CYS CYS ASP SEQRES 7 A 141 PHE CYS HIS ASN ALA PHE CYS LYS LYS CYS ILE LEU ARG SEQRES 8 A 141 ASN LEU GLY ARG LYS GLU LEU SER THR ILE MET ASP GLU SEQRES 9 A 141 ASN ASN GLN TRP TYR CYS TYR ILE CYS HIS PRO GLU PRO SEQRES 10 A 141 LEU LEU ASP LEU VAL THR ALA CYS ASN SER VAL PHE GLU SEQRES 11 A 141 ASN LEU GLU GLN LEU LEU GLN GLN ASN LYS LYS HET ZN A 1 1 HET ZN A 2 1 HET ZN A 3 1 HETNAM ZN ZINC ION FORMUL 2 ZN 3(ZN 2+) HELIX 1 1 CYS A 197 ASP A 207 1 11 HELIX 2 2 LYS A 241 GLY A 249 1 9 HELIX 3 3 ARG A 250 MET A 257 1 8 HELIX 4 4 LEU A 273 GLN A 292 1 20 SHEET 1 A 2 TYR A 187 ARG A 188 0 SHEET 2 A 2 LEU A 195 ILE A 196 -1 O ILE A 196 N TYR A 187 SHEET 1 B 2 LEU A 229 CYS A 231 0 SHEET 2 B 2 ALA A 238 CYS A 240 -1 O PHE A 239 N ILE A 230 LINK ZN ZN A 1 SG CYS A 171 1555 1555 2.31 LINK ZN ZN A 1 SG CYS A 174 1555 1555 2.31 LINK ZN ZN A 1 SG CYS A 197 1555 1555 2.31 LINK ZN ZN A 1 SG CYS A 200 1555 1555 2.30 LINK ZN ZN A 2 SG CYS A 220 1555 1555 2.29 LINK ZN ZN A 2 SG CYS A 223 1555 1555 2.31 LINK ZN ZN A 2 SG CYS A 240 1555 1555 2.30 LINK ZN ZN A 2 SG CYS A 243 1555 1555 2.31 LINK ZN ZN A 3 SG CYS A 232 1555 1555 2.30 LINK ZN ZN A 3 SG CYS A 235 1555 1555 2.30 LINK ZN ZN A 3 SG CYS A 265 1555 1555 2.30 LINK ZN ZN A 3 SG CYS A 268 1555 1555 2.31 SITE 1 AC1 4 CYS A 171 CYS A 174 CYS A 197 CYS A 200 SITE 1 AC2 4 CYS A 220 CYS A 223 CYS A 240 CYS A 243 SITE 1 AC3 4 CYS A 232 CYS A 235 CYS A 265 CYS A 268 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