HEADER TRANSCRIPTION REGULATOR 12-SEP-14 2MUM TITLE SOLUTION STRUCTURE OF THE PHD DOMAIN OF YEAST YNG2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMATIN MODIFICATION-RELATED PROTEIN YNG2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD-TYPE DOMAIN RESIDUES 222-271; COMPND 5 SYNONYM: ESA1-ASSOCIATED FACTOR 4, ING1 HOMOLOG 2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: YNG2, EAF4, NBN1, YHR090C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS PHD FINGER, TRANSCRIPTION REGULATOR EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.TAEB,L.KAUSTOV,A.LEMAK,S.FARHADI,Y.SHENG REVDAT 2 14-JUN-23 2MUM 1 REMARK LINK REVDAT 1 24-DEC-14 2MUM 0 JRNL AUTH S.TAEB,L.KAUSTOV,A.LEMAK,S.FARHADI,Y.SHENG JRNL TITL SOLUTION STRUCTURE OF THE PHD DOMAIN OF YEAST YNG2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, FMCGUI, CNSSOLVE, CNS REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), LEMAK A., GUTMANAS A., REMARK 3 CHITAYAT S., KARRA M., FAR S C., SUNNERHAGEN M., REMARK 3 AND ARROWSMITH C.H. (FMCGUI), BRUNGER, ADAMS, REMARK 3 CLORE, GROS, NILGES AND READ (CNSSOLVE), BRUNGER, REMARK 3 ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MUM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000104064. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 300 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-13C; U-15N] PROTEIN, REMARK 210 300 MM SODIUM CHLORIDE, 2.7 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM REMARK 210 POTASSIUM PHOSPHATE, 10 MM REMARK 210 SODIUM PHOSPHATE, 0.05 MM CHAPS, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D HNCA; 3D CBCA(CO)NH; REMARK 210 3D HCCH-TOCSY; 3D HBHA(CO)NH; 3D REMARK 210 HNCO; 2D 1H-15N HSQC; 2D 1H-13C REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY, FMCGUI, CYANA REMARK 210 METHOD USED : MOLECULAR 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: 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: 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 CYS A 225 163.03 173.26 REMARK 500 1 GLN A 228 85.95 48.67 REMARK 500 1 CYS A 243 102.82 -173.07 REMARK 500 1 ASN A 254 70.91 58.73 REMARK 500 2 CYS A 225 166.90 172.75 REMARK 500 2 GLN A 228 77.61 48.66 REMARK 500 2 PHE A 232 66.54 -112.23 REMARK 500 2 CYS A 243 110.90 -173.23 REMARK 500 3 CYS A 225 152.18 171.25 REMARK 500 3 GLN A 228 85.82 57.12 REMARK 500 3 TYR A 245 31.11 -82.72 REMARK 500 4 CYS A 225 160.07 172.48 REMARK 500 4 GLN A 228 78.94 54.88 REMARK 500 4 CYS A 243 116.74 -171.98 REMARK 500 4 TYR A 245 29.92 -79.28 REMARK 500 5 CYS A 225 163.32 170.21 REMARK 500 5 GLN A 228 77.40 51.82 REMARK 500 5 ASN A 242 77.65 -107.49 REMARK 500 5 ILE A 270 -72.06 -95.66 REMARK 500 6 CYS A 225 158.47 170.58 REMARK 500 6 GLN A 228 81.15 50.01 REMARK 500 6 ASN A 242 70.81 -110.81 REMARK 500 6 CYS A 243 107.08 -167.40 REMARK 500 6 TYR A 245 24.77 -79.62 REMARK 500 6 PRO A 266 -63.00 -23.67 REMARK 500 7 CYS A 225 162.86 172.47 REMARK 500 7 GLN A 228 85.58 54.99 REMARK 500 7 PRO A 259 172.92 -58.69 REMARK 500 8 CYS A 225 161.32 172.96 REMARK 500 8 GLN A 228 81.71 52.37 REMARK 500 8 CYS A 243 107.51 -167.94 REMARK 500 8 PRO A 266 -70.11 -19.09 REMARK 500 9 CYS A 225 153.13 172.20 REMARK 500 9 GLN A 228 80.55 54.09 REMARK 500 9 CYS A 243 81.15 -168.75 REMARK 500 10 CYS A 225 163.84 171.80 REMARK 500 10 GLN A 228 81.86 46.45 REMARK 500 10 SER A 231 77.72 -100.86 REMARK 500 10 CYS A 243 112.15 -172.17 REMARK 500 10 TYR A 245 27.47 -79.33 REMARK 500 10 PRO A 266 -64.88 -23.70 REMARK 500 11 CYS A 225 158.08 174.08 REMARK 500 11 SER A 231 69.18 -105.66 REMARK 500 11 CYS A 243 101.80 -166.06 REMARK 500 11 ASN A 254 70.12 52.41 REMARK 500 11 PRO A 266 -38.80 -36.63 REMARK 500 12 CYS A 225 155.69 172.29 REMARK 500 12 GLN A 228 85.46 52.16 REMARK 500 12 CYS A 243 104.60 -174.75 REMARK 500 12 LYS A 256 -29.97 -145.86 REMARK 500 REMARK 500 THIS ENTRY HAS 80 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 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 225 SG REMARK 620 2 CYS A 227 SG 109.9 REMARK 620 3 HIS A 249 NE2 105.9 109.7 REMARK 620 4 CYS A 252 SG 110.3 114.9 105.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 238 SG REMARK 620 2 CYS A 243 SG 111.5 REMARK 620 3 CYS A 265 SG 107.6 110.3 REMARK 620 4 CYS A 268 SG 108.8 109.3 109.3 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25221 RELATED DB: BMRB DBREF 2MUM A 222 271 UNP P38806 YNG2_YEAST 222 271 SEQRES 1 A 50 THR LEU TYR CYS PHE CYS GLN ARG VAL SER PHE GLY GLU SEQRES 2 A 50 MET VAL ALA CYS ASP GLY PRO ASN CYS LYS TYR GLU TRP SEQRES 3 A 50 PHE HIS TYR ASP CYS VAL ASN LEU LYS GLU PRO PRO LYS SEQRES 4 A 50 GLY THR TRP TYR CYS PRO GLU CYS LYS ILE GLU HET ZN A 301 1 HET ZN A 302 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 CYS A 265 GLU A 271 1 7 SHEET 1 A 2 VAL A 236 ALA A 237 0 SHEET 2 A 2 TRP A 247 PHE A 248 -1 O PHE A 248 N VAL A 236 LINK SG CYS A 225 ZN ZN A 301 1555 1555 2.31 LINK SG CYS A 227 ZN ZN A 301 1555 1555 2.36 LINK SG CYS A 238 ZN ZN A 302 1555 1555 2.33 LINK SG CYS A 243 ZN ZN A 302 1555 1555 2.35 LINK NE2 HIS A 249 ZN ZN A 301 1555 1555 2.09 LINK SG CYS A 252 ZN ZN A 301 1555 1555 2.34 LINK SG CYS A 265 ZN ZN A 302 1555 1555 2.31 LINK SG CYS A 268 ZN ZN A 302 1555 1555 2.34 SITE 1 AC1 4 CYS A 225 CYS A 227 HIS A 249 CYS A 252 SITE 1 AC2 4 CYS A 238 CYS A 243 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 MODEL 1