HEADER GENE REGULATION 05-DEC-12 2M1R TITLE PHD DOMAIN OF ING4 N214D MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: INHIBITOR OF GROWTH PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: P29ING4; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 VARIANT: ISOFORM 1; SOURCE 6 GENE: ING4, MY036; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET11D KEYWDS ING4, PHD, TRANSCRIPTION, GENE REGULATION EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR F.J.BLANCO REVDAT 1 26-DEC-12 2M1R 0 JRNL AUTH A.MORENO,A.PALACIOS,J.L.ORGAZ,B.JIMENEZ,F.J.BLANCO,I.PALMERO JRNL TITL FUNCTIONAL IMPACT OF CANCER-ASSOCIATED MUTATIONS IN THE JRNL TITL 2 TUMOR SUPPRESSOR PROTEIN ING4. JRNL REF CARCINOGENESIS V. 31 1932 2010 JRNL REFN JRNL PMID 20705953 JRNL DOI 10.1093/CARCIN/BGQ171 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, CYANA REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO AND KOLLMAN (AMBER), GUNTERT, MUMENTHALER REMARK 3 AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATED ANNEALING COMBINED WITH REMARK 3 TORSION ANGLE DYNAMICS. ITERATIVE CYCLES OF STRUCTURE CALCULATION REMARK 3 AND NOE ASSIGNMENT. ENERGY MINIMIZATION IN VACUO WITH IMPLICIT REMARK 3 SOLVENT (DISTANCE DEPENDENT DIELECRIC CONSTANT) REMARK 4 REMARK 4 2M1R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-12. REMARK 100 THE RCSB ID CODE IS RCSB103099. 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 : 70 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 15N] ING4 PHD REMARK 210 MUTANT N214D, 30 UM DSS, 1 MM REMARK 210 DTT, 20 MM SODIUM PHOSPHATE, 50 REMARK 210 MM SODIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-1H NOESY; REMARK 210 3D 1H-15N NOESY; 3D 1H-15N TOCSY; REMARK 210 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, NMRPIPE, NMRDRAW, REMARK 210 NMRVIEW, CYANA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 ASP A 188 -43.62 -154.80 REMARK 500 1 MET A 189 62.38 33.40 REMARK 500 1 THR A 197 147.00 64.14 REMARK 500 1 TYR A 198 -43.95 -154.74 REMARK 500 1 CYS A 199 169.66 -38.05 REMARK 500 1 SER A 205 60.89 66.69 REMARK 500 1 ILE A 210 -139.64 -138.00 REMARK 500 1 ILE A 219 -35.53 -132.58 REMARK 500 1 GLU A 220 -42.90 72.44 REMARK 500 1 THR A 230 -17.42 63.87 REMARK 500 1 ARG A 234 -176.60 -175.31 REMARK 500 1 PRO A 240 35.23 -73.06 REMARK 500 1 ARG A 241 -38.37 -137.95 REMARK 500 2 ASN A 194 57.93 -150.49 REMARK 500 2 TYR A 198 -45.39 -155.04 REMARK 500 2 CYS A 199 169.66 -38.01 REMARK 500 2 SER A 205 63.47 65.44 REMARK 500 2 TYR A 206 112.55 -163.07 REMARK 500 2 ILE A 210 -138.51 -139.02 REMARK 500 2 ASP A 213 1.40 -66.85 REMARK 500 2 ILE A 219 -35.33 -133.78 REMARK 500 2 GLU A 220 -39.53 72.91 REMARK 500 2 THR A 230 -10.42 62.16 REMARK 500 2 LYS A 236 74.84 40.30 REMARK 500 2 PRO A 240 28.66 -72.41 REMARK 500 2 ARG A 241 -32.95 -136.02 REMARK 500 2 ARG A 246 54.59 39.16 REMARK 500 2 LYS A 248 35.18 -146.96 REMARK 500 3 PRO A 190 24.04 -79.90 REMARK 500 3 ASP A 192 -46.50 -131.83 REMARK 500 3 ASN A 194 -15.82 -142.23 REMARK 500 3 TYR A 198 -46.53 -155.15 REMARK 500 3 CYS A 199 169.54 -37.46 REMARK 500 3 SER A 205 61.68 66.33 REMARK 500 3 TYR A 206 114.10 -161.98 REMARK 500 3 ILE A 210 -139.61 -138.56 REMARK 500 3 ILE A 219 -34.96 -132.96 REMARK 500 3 GLU A 220 -39.31 72.34 REMARK 500 3 PRO A 240 36.79 -73.67 REMARK 500 3 ARG A 241 -39.62 -139.96 REMARK 500 3 ARG A 246 78.08 -157.89 REMARK 500 3 LYS A 247 93.25 -69.99 REMARK 500 4 GLU A 195 99.22 -31.93 REMARK 500 4 THR A 197 142.78 66.17 REMARK 500 4 TYR A 198 -37.89 -154.93 REMARK 500 4 CYS A 199 172.61 -52.88 REMARK 500 4 SER A 205 63.93 65.19 REMARK 500 4 TYR A 206 112.23 -165.59 REMARK 500 4 ILE A 210 -136.18 -142.04 REMARK 500 4 ILE A 219 -37.19 -135.76 REMARK 500 REMARK 500 THIS ENTRY HAS 346 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 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 206 OH REMARK 620 2 CYS A 201 SG 92.1 REMARK 620 3 CYS A 226 SG 167.7 89.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 217 SG REMARK 620 2 CYS A 239 SG 147.9 REMARK 620 N 1 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: 2K1J RELATED DB: PDB REMARK 900 STRUCTURE OF THE WT PHD DOMAIN OF ING4 REMARK 900 RELATED ID: 2VNF RELATED DB: PDB REMARK 900 STRUCTURE OF THE WT PHD DOMAIN OF ING4 BOUND TO HISTONE H3 REMARK 900 PEPTIDE WITH K4ME3 REMARK 900 RELATED ID: 4AFL RELATED DB: PDB REMARK 900 STRUCTURE OF THE N-TERMINAL DIMERIZATION DOMAIN OF ING4 REMARK 900 RELATED ID: 1PNX RELATED DB: PDB REMARK 900 STRUCTURE OF THE WT PHD DOMAIN OF ING4 BOUND TO HISTONE H3 REMARK 900 PEPTIDE WITH K4ME3 REMARK 900 RELATED ID: 18874 RELATED DB: BMRB DBREF 2M1R A 188 249 UNP Q9UNL4 ING4_HUMAN 188 249 SEQADV 2M1R MET A 187 UNP Q9UNL4 EXPRESSION TAG SEQADV 2M1R ASP A 214 UNP Q9UNL4 ASN 214 ENGINEERED MUTATION SEQRES 1 A 63 MET ASP MET PRO VAL ASP PRO ASN GLU PRO THR TYR CYS SEQRES 2 A 63 LEU CYS HIS GLN VAL SER TYR GLY GLU MET ILE GLY CYS SEQRES 3 A 63 ASP ASP PRO ASP CYS SER ILE GLU TRP PHE HIS PHE ALA SEQRES 4 A 63 CYS VAL GLY LEU THR THR LYS PRO ARG GLY LYS TRP PHE SEQRES 5 A 63 CYS PRO ARG CYS SER GLN GLU ARG LYS LYS LYS HET ZN A 301 1 HET ZN A 302 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 SER A 243 LYS A 247 5 5 LINK OH TYR A 206 ZN ZN A 301 1555 1555 2.18 LINK SG CYS A 217 ZN ZN A 302 1555 1555 2.35 LINK SG CYS A 239 ZN ZN A 302 1555 1555 2.39 LINK SG CYS A 201 ZN ZN A 301 1555 1555 2.49 LINK SG CYS A 226 ZN ZN A 301 1555 1555 2.54 SITE 1 AC1 5 CYS A 199 CYS A 201 TYR A 206 HIS A 223 SITE 2 AC1 5 CYS A 226 SITE 1 AC2 5 CYS A 212 CYS A 217 PHE A 222 CYS A 239 SITE 2 AC2 5 CYS A 242 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