PDB Short entry for 2KWN HEADER METAL BINDING PROTEIN 13-APR-10 2KWN TITLE SOLUTION STRUCTURE OF THE DOUBLE PHD (PLANT HOMEODOMAIN) FINGERS OF TITLE 2 HUMAN TRANSCRIPTIONAL PROTEIN DPF3B BOUND TO A HISTONE H4 PEPTIDE TITLE 3 CONTAINING ACETYLATION AT LYSINE 16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE PEPTIDE; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ZINC FINGER PROTEIN DPF3; COMPND 7 CHAIN: A; COMPND 8 FRAGMENT: PHD-TYPES 1 AND 2 RESIDUES 261-372; COMPND 9 SYNONYM: ZINC FINGER PROTEIN CER-D4, BRG1-ASSOCIATED FACTOR 45C, COMPND 10 BAF45C; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 6 ORGANISM_COMMON: HUMAN; SOURCE 7 ORGANISM_TAXID: 9606; SOURCE 8 GENE: DPF3, BAF45C, CERD4; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 12 EXPRESSION_SYSTEM_VECTOR: PGEX4T-1 KEYWDS ACETYL-LYSINE, TRANSCRIPTION REGULATION, NUCLEUS, METAL BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.ZENG,Q.ZHANG,S.LI,A.N.PLOTNIKOV,M.J.WALSH,M.ZHOU REVDAT 3 15-NOV-23 2KWN 1 REMARK DBREF SEQADV LINK REVDAT 3 2 1 ATOM REVDAT 2 19-JUN-13 2KWN 1 JRNL VERSN DBREF REVDAT 1 14-JUL-10 2KWN 0 JRNL AUTH L.ZENG,Q.ZHANG,S.LI,A.N.PLOTNIKOV,M.J.WALSH,M.M.ZHOU JRNL TITL MECHANISM AND REGULATION OF ACETYLATED HISTONE BINDING BY JRNL TITL 2 THE TANDEM PHD FINGER OF DPF3B. JRNL REF NATURE V. 466 258 2010 JRNL REFN ISSN 0028-0836 JRNL PMID 20613843 JRNL DOI 10.1038/NATURE09139 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KWN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000101665. 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 : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 100 MM SODIUM PHOSPHATE, 2 MM REMARK 210 DTT, 100% D2O; 100 MM SODIUM REMARK 210 PHOSPHATE, 2 MM DTT, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D HN(COCA)CB; 3D 1H REMARK 210 -15N NOESY; 3D 1H-13C NOESY; 3D_ REMARK 210 13C-EDITED_13C/15N-FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 600 MHZ; 500 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, NMRVIEW 5.04, CNS REMARK 210 1.2 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING, TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 HG23 VAL A 350 H ALA A 351 1.34 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 16 PRO A 353 C - N - CA ANGL. DEV. = 9.1 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 ALA B 15 -88.86 -144.75 REMARK 500 1 ALY B 16 -45.43 -172.29 REMARK 500 1 ARG B 17 172.39 57.72 REMARK 500 1 HIS B 18 -139.41 -61.85 REMARK 500 1 ARG B 19 -24.87 83.45 REMARK 500 1 LYS B 20 103.37 44.91 REMARK 500 1 LEU B 22 89.50 58.39 REMARK 500 1 SER A 260 -171.74 56.47 REMARK 500 1 ASN A 270 22.26 -159.48 REMARK 500 1 MET A 271 102.89 -171.60 REMARK 500 1 GLU A 279 -137.25 -159.09 REMARK 500 1 GLU A 280 90.28 -172.81 REMARK 500 1 LEU A 281 178.66 -53.56 REMARK 500 1 PHE A 298 178.31 -59.04 REMARK 500 1 TYR A 309 -161.67 -107.05 REMARK 500 1 TRP A 311 -57.40 80.05 REMARK 500 1 GLN A 312 116.32 55.21 REMARK 500 1 LYS A 317 166.30 -38.01 REMARK 500 1 CYS A 322 -60.65 -90.34 REMARK 500 1 SER A 325 15.77 51.49 REMARK 500 1 GLU A 326 -81.53 -50.93 REMARK 500 1 ASN A 327 41.05 -78.44 REMARK 500 1 ASP A 328 -19.30 -41.90 REMARK 500 1 ASP A 335 36.34 -78.98 REMARK 500 1 CYS A 337 -18.85 175.10 REMARK 500 1 ASP A 338 -19.78 94.08 REMARK 500 1 MET A 343 -29.50 -32.96 REMARK 500 1 LEU A 346 179.22 -54.87 REMARK 500 1 PRO A 348 56.66 -114.35 REMARK 500 1 PRO A 349 150.95 -27.50 REMARK 500 1 GLU A 352 -50.94 -166.86 REMARK 500 1 PRO A 353 -51.65 -10.37 REMARK 500 1 PRO A 354 47.50 -76.29 REMARK 500 1 SER A 357 -115.74 -65.15 REMARK 500 1 TRP A 358 154.59 69.46 REMARK 500 1 CYS A 360 -178.58 46.46 REMARK 500 1 ALA A 371 174.07 -56.77 REMARK 500 2 LYS B 12 88.20 -154.43 REMARK 500 2 ALY B 16 -58.14 -150.04 REMARK 500 2 ARG B 17 -98.55 58.81 REMARK 500 2 HIS B 18 -144.85 -144.47 REMARK 500 2 ARG B 19 -11.67 71.10 REMARK 500 2 LYS B 20 -154.00 40.24 REMARK 500 2 LEU B 22 -11.03 -166.29 REMARK 500 2 ASP A 263 2.71 -69.44 REMARK 500 2 ASN A 270 17.93 -147.33 REMARK 500 2 MET A 271 115.76 -169.02 REMARK 500 2 GLU A 279 -131.85 -150.44 REMARK 500 2 GLU A 280 90.12 -177.56 REMARK 500 2 LEU A 281 173.35 -49.18 REMARK 500 REMARK 500 THIS ENTRY HAS 744 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 19 ARG A 339 0.15 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 262 SG REMARK 620 2 CYS A 265 SG 115.2 REMARK 620 3 HIS A 292 ND1 97.8 112.2 REMARK 620 4 CYS A 295 SG 114.0 109.3 107.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 284 SG REMARK 620 2 CYS A 287 SG 108.7 REMARK 620 3 CYS A 313 SG 109.9 109.3 REMARK 620 4 CYS A 316 SG 109.1 111.5 108.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 319 SG REMARK 620 2 CYS A 322 SG 112.1 REMARK 620 3 HIS A 342 ND1 101.5 108.6 REMARK 620 4 CYS A 345 SG 116.0 109.7 108.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 334 SG REMARK 620 2 CYS A 337 SG 108.6 REMARK 620 3 CYS A 360 SG 109.2 109.5 REMARK 620 4 CYS A 363 SG 109.7 109.5 110.4 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 801 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KWJ RELATED DB: PDB REMARK 900 DPF3B PHD WITH H3 PEPTIDE AT ALY14 REMARK 900 RELATED ID: 2KWK RELATED DB: PDB REMARK 900 DPF3B PHD WITH H3 PEPTIDE IN WILD TYPE REMARK 900 RELATED ID: 2KWO RELATED DB: PDB REMARK 900 DPF3 PHD WITH H4 PEPTIDE AT N-TERMINAL ACTYL-SERINE DBREF 2KWN B 9 23 PDB 2KWN 2KWN 9 23 DBREF 2KWN A 261 372 UNP Q92784 DPF3_HUMAN 261 372 SEQADV 2KWN GLY A 259 UNP Q92784 EXPRESSION TAG SEQADV 2KWN SER A 260 UNP Q92784 EXPRESSION TAG SEQRES 1 B 15 GLY LEU GLY LYS GLY GLY ALA ALY ARG HIS ARG LYS VAL SEQRES 2 B 15 LEU ARG SEQRES 1 A 114 GLY SER TYR CYS ASP PHE CYS LEU GLY GLY SER ASN MET SEQRES 2 A 114 ASN LYS LYS SER GLY ARG PRO GLU GLU LEU VAL SER CYS SEQRES 3 A 114 ALA ASP CYS GLY ARG SER GLY HIS PRO THR CYS LEU GLN SEQRES 4 A 114 PHE THR LEU ASN MET THR GLU ALA VAL LYS THR TYR LYS SEQRES 5 A 114 TRP GLN CYS ILE GLU CYS LYS SER CYS ILE LEU CYS GLY SEQRES 6 A 114 THR SER GLU ASN ASP ASP GLN LEU LEU PHE CYS ASP ASP SEQRES 7 A 114 CYS ASP ARG GLY TYR HIS MET TYR CYS LEU ASN PRO PRO SEQRES 8 A 114 VAL ALA GLU PRO PRO GLU GLY SER TRP SER CYS HIS LEU SEQRES 9 A 114 CYS TRP GLU LEU LEU LYS GLU LYS ALA SER MODRES 2KWN ALY B 16 LYS N(6)-ACETYLLYSINE HET ALY B 16 26 HET ZN A 501 1 HET ZN A 601 1 HET ZN A 701 1 HET ZN A 801 1 HETNAM ALY N(6)-ACETYLLYSINE HETNAM ZN ZINC ION FORMUL 1 ALY C8 H16 N2 O3 FORMUL 3 ZN 4(ZN 2+) HELIX 1 1 HIS A 292 GLN A 297 1 6 HELIX 2 2 THR A 299 TYR A 309 1 11 HELIX 3 3 CYS A 313 LYS A 317 5 5 HELIX 4 4 SER A 359 ALA A 371 1 13 SHEET 1 A 2 LEU A 331 PHE A 333 0 SHEET 2 A 2 GLY A 340 HIS A 342 -1 O TYR A 341 N LEU A 332 LINK C ALA B 15 N ALY B 16 1555 1555 1.33 LINK C ALY B 16 N ARG B 17 1555 1555 1.33 LINK SG CYS A 262 ZN ZN A 501 1555 1555 2.29 LINK SG CYS A 265 ZN ZN A 501 1555 1555 2.32 LINK SG CYS A 284 ZN ZN A 601 1555 1555 2.32 LINK SG CYS A 287 ZN ZN A 601 1555 1555 2.32 LINK ND1 HIS A 292 ZN ZN A 501 1555 1555 2.08 LINK SG CYS A 295 ZN ZN A 501 1555 1555 2.32 LINK SG CYS A 313 ZN ZN A 601 1555 1555 2.32 LINK SG CYS A 316 ZN ZN A 601 1555 1555 2.32 LINK SG CYS A 319 ZN ZN A 801 1555 1555 2.31 LINK SG CYS A 322 ZN ZN A 801 1555 1555 2.32 LINK SG CYS A 334 ZN ZN A 701 1555 1555 2.31 LINK SG CYS A 337 ZN ZN A 701 1555 1555 2.32 LINK ND1 HIS A 342 ZN ZN A 801 1555 1555 2.08 LINK SG CYS A 345 ZN ZN A 801 1555 1555 2.32 LINK SG CYS A 360 ZN ZN A 701 1555 1555 2.32 LINK SG CYS A 363 ZN ZN A 701 1555 1555 2.33 SITE 1 AC1 5 CYS A 262 PHE A 264 CYS A 265 HIS A 292 SITE 2 AC1 5 CYS A 295 SITE 1 AC2 4 CYS A 284 CYS A 287 CYS A 313 CYS A 316 SITE 1 AC3 5 CYS A 334 CYS A 337 SER A 359 CYS A 360 SITE 2 AC3 5 CYS A 363 SITE 1 AC4 4 CYS A 319 CYS A 322 HIS A 342 CYS A 345 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