PDB Short entry for 5Y0U HEADER METAL BINDING PROTEIN 18-JUL-17 5Y0U TITLE THE SOLUTION STRUCTURE OF AEBP2 C2H2 ZINC FINGERS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER PROTEIN AEBP2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 258-357; COMPND 5 SYNONYM: ADIPOCYTE ENHANCER-BINDING PROTEIN 2,AE-BINDING PROTEIN 2; COMPND 6 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: AEBP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3)PLYSS AG; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P28 KEYWDS C2H2, AEBP2, PRC2, ZINC FINGER, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.SUN,Y.SHI,J.WU REVDAT 2 14-JUN-23 5Y0U 1 REMARK REVDAT 1 01-AUG-18 5Y0U 0 JRNL AUTH A.SUN,F.LI,Z.LIU,Y.JIANG,J.ZHANG,J.WU,Y.SHI JRNL TITL STRUCTURAL AND BIOCHEMICAL INSIGHTS INTO HUMAN ZINC FINGER JRNL TITL 2 PROTEIN AEBP2 REVEALS INTERACTIONS WITH RBBP4. JRNL REF PROTEIN CELL V. 9 738 2018 JRNL REFN ESSN 1674-8018 JRNL PMID 29134516 JRNL DOI 10.1007/S13238-017-0483-6 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5Y0U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1300004460. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.3 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 101325 PA REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-99% 13C; U-99% 15N] REMARK 210 ZINC FINGER PROTEIN AEBP2, 5 MM REMARK 210 [U-0% 13C; U-0% 15N] DTT, 0.025 REMARK 210 MM [U-0% 13C; U-0% 15N] TRIS, REMARK 210 0.1 MM [U-0% 13C; U-0% 15N] REMARK 210 SODIUM CHLORIDE, 90% H2O/10% D2O; REMARK 210 0.8 MM [U-0% 13C; U-0% 15N] REMARK 210 ZINC FINGER PROTEIN AEBP2, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, SPARKY REMARK 210 METHOD USED : NA 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: 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 HIS A 254 167.68 64.53 REMARK 500 1 ASP A 266 93.50 -24.16 REMARK 500 1 HIS A 286 -69.18 -100.86 REMARK 500 1 LYS A 326 -65.29 -122.89 REMARK 500 1 PHE A 353 46.61 -92.08 REMARK 500 1 GLN A 356 -65.52 72.65 REMARK 500 2 HIS A 254 -77.79 -97.67 REMARK 500 2 HIS A 256 169.81 71.84 REMARK 500 2 CYS A 264 70.13 -113.33 REMARK 500 2 ASP A 266 85.45 -17.70 REMARK 500 2 HIS A 286 -63.93 -99.58 REMARK 500 2 ARG A 291 29.43 -72.91 REMARK 500 2 PRO A 327 108.83 -37.39 REMARK 500 2 GLN A 356 -50.30 68.83 REMARK 500 3 HIS A 253 -155.76 -115.07 REMARK 500 3 ASP A 266 -139.44 61.74 REMARK 500 3 HIS A 286 -65.34 -102.32 REMARK 500 3 LYS A 326 -62.59 -144.97 REMARK 500 3 GLN A 356 63.79 67.83 REMARK 500 4 HIS A 252 -38.03 77.15 REMARK 500 4 HIS A 255 92.33 67.32 REMARK 500 4 ASN A 258 134.58 76.50 REMARK 500 4 ALA A 260 -138.52 63.71 REMARK 500 4 GLN A 267 5.28 82.03 REMARK 500 4 HIS A 286 -68.93 -100.65 REMARK 500 4 ASN A 306 31.46 71.21 REMARK 500 4 ASP A 325 -155.04 -104.60 REMARK 500 4 LYS A 326 -59.92 -151.04 REMARK 500 5 HIS A 252 117.65 -177.51 REMARK 500 5 HIS A 253 103.52 68.21 REMARK 500 5 ASN A 257 71.16 56.52 REMARK 500 5 ASP A 266 -142.89 61.25 REMARK 500 5 GLN A 267 74.48 -104.31 REMARK 500 5 HIS A 286 -62.28 -106.60 REMARK 500 5 LYS A 326 -62.98 -159.67 REMARK 500 6 HIS A 254 -168.07 -106.93 REMARK 500 6 ILE A 259 163.65 84.39 REMARK 500 6 ASP A 266 65.10 33.12 REMARK 500 6 GLN A 267 13.22 80.81 REMARK 500 6 HIS A 286 -64.76 -106.07 REMARK 500 6 ARG A 291 84.12 -62.85 REMARK 500 6 LYS A 326 -59.42 -144.55 REMARK 500 6 SER A 354 -64.15 73.87 REMARK 500 7 HIS A 253 76.62 67.07 REMARK 500 7 HIS A 255 -64.70 -100.05 REMARK 500 7 ASN A 258 -149.00 55.80 REMARK 500 7 HIS A 286 -64.00 -105.09 REMARK 500 8 HIS A 255 -81.53 60.14 REMARK 500 8 ASN A 257 -76.53 -64.85 REMARK 500 8 ASN A 258 82.22 41.90 REMARK 500 REMARK 500 THIS ENTRY HAS 128 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 291 0.07 SIDE CHAIN REMARK 500 5 ARG A 283 0.07 SIDE CHAIN REMARK 500 10 ARG A 317 0.09 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 281 NE2 REMARK 620 2 HIS A 286 NE2 85.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 318 NE2 REMARK 620 2 HIS A 322 NE2 89.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 348 NE2 REMARK 620 2 HIS A 352 NE2 88.1 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36108 RELATED DB: BMRB REMARK 900 THE SOLUTION STRUCTURE OF AEBP2 C2H2 ZINC FINGERS DBREF 5Y0U A 258 357 UNP Q6ZN18 AEBP2_HUMAN 258 357 SEQADV 5Y0U MET A 249 UNP Q6ZN18 EXPRESSION TAG SEQADV 5Y0U GLY A 250 UNP Q6ZN18 EXPRESSION TAG SEQADV 5Y0U HIS A 251 UNP Q6ZN18 EXPRESSION TAG SEQADV 5Y0U HIS A 252 UNP Q6ZN18 EXPRESSION TAG SEQADV 5Y0U HIS A 253 UNP Q6ZN18 EXPRESSION TAG SEQADV 5Y0U HIS A 254 UNP Q6ZN18 EXPRESSION TAG SEQADV 5Y0U HIS A 255 UNP Q6ZN18 EXPRESSION TAG SEQADV 5Y0U HIS A 256 UNP Q6ZN18 EXPRESSION TAG SEQADV 5Y0U ASN A 257 UNP Q6ZN18 EXPRESSION TAG SEQRES 1 A 109 MET GLY HIS HIS HIS HIS HIS HIS ASN ASN ILE ALA TYR SEQRES 2 A 109 ASN CYS CYS TRP ASP GLN CYS GLN ALA CYS PHE ASN SER SEQRES 3 A 109 SER PRO ASP LEU ALA ASP HIS ILE ARG SER ILE HIS VAL SEQRES 4 A 109 ASP GLY GLN ARG GLY GLY VAL PHE VAL CYS LEU TRP LYS SEQRES 5 A 109 GLY CYS LYS VAL TYR ASN THR PRO SER THR SER GLN SER SEQRES 6 A 109 TRP LEU GLN ARG HIS MET LEU THR HIS SER GLY ASP LYS SEQRES 7 A 109 PRO PHE LYS CYS VAL VAL GLY GLY CYS ASN ALA SER PHE SEQRES 8 A 109 ALA SER GLN GLY GLY LEU ALA ARG HIS VAL PRO THR HIS SEQRES 9 A 109 PHE SER GLN GLN ASN HET ZN A 401 1 HET ZN A 402 1 HET ZN A 403 1 HETNAM ZN ZINC ION FORMUL 2 ZN 3(ZN 2+) HELIX 1 AA1 SER A 274 HIS A 286 1 13 HELIX 2 AA2 VAL A 287 ARG A 291 5 5 HELIX 3 AA3 SER A 311 GLY A 324 1 14 HELIX 4 AA4 SER A 341 PHE A 353 1 13 SHEET 1 AA1 2 TYR A 261 ASN A 262 0 SHEET 2 AA1 2 CYS A 271 PHE A 272 -1 O PHE A 272 N TYR A 261 SHEET 1 AA2 2 PHE A 328 LYS A 329 0 SHEET 2 AA2 2 SER A 338 PHE A 339 -1 O PHE A 339 N PHE A 328 LINK NE2 HIS A 281 ZN ZN A 401 1555 1555 1.94 LINK NE2 HIS A 286 ZN ZN A 401 1555 1555 2.33 LINK NE2 HIS A 318 ZN ZN A 402 1555 1555 1.93 LINK NE2 HIS A 322 ZN ZN A 402 1555 1555 2.30 LINK NE2 HIS A 348 ZN ZN A 403 1555 1555 1.85 LINK NE2 HIS A 352 ZN ZN A 403 1555 1555 2.30 SITE 1 AC1 5 CYS A 263 CYS A 268 ALA A 270 HIS A 281 SITE 2 AC1 5 HIS A 286 SITE 1 AC2 5 CYS A 297 TRP A 299 CYS A 302 HIS A 318 SITE 2 AC2 5 HIS A 322 SITE 1 AC3 4 CYS A 330 CYS A 335 HIS A 348 HIS A 352 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