PDB Short entry for 2LGK HEADER LIGASE/DNA BINDING PROTEIN 28-JUL-11 2LGK TITLE NMR STRUCTURE OF UHRF1 PHD DOMAINS IN A COMPLEX WITH HISTONE H3 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE UHRF1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 298-366; COMPND 5 SYNONYM: INVERTED CCAAT BOX-BINDING PROTEIN OF 90 KDA, NUCLEAR COMPND 6 PROTEIN 95, NUCLEAR ZINC FINGER PROTEIN NP95, HUNP95, RING FINGER COMPND 7 PROTEIN 106, TRANSCRIPTION FACTOR ICBP90, UBIQUITIN-LIKE PHD AND RING COMPND 8 FINGER DOMAIN-CONTAINING PROTEIN 1, UBIQUITIN-LIKE-CONTAINING PHD AND COMPND 9 RING FINGER DOMAINS PROTEIN 1; COMPND 10 EC: 6.3.2.-; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 2; COMPND 13 MOLECULE: HISTONE H3 PEPTIDE; COMPND 14 CHAIN: B; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PETDUET; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. KEYWDS UHRF1, PHD, HISTONE H3, LIGASE-DNA BINDING PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.WANG,J.SHEN,Z.YANG,P.CHEN,B.ZHAO,W.HU,W.LAN,X.TONG,H.WU,G.LI,C.CAO REVDAT 2 14-JUN-23 2LGK 1 REMARK LINK REVDAT 1 28-SEP-11 2LGK 0 JRNL AUTH C.WANG,J.SHEN,Z.YANG,P.CHEN,B.ZHAO,W.HU,W.LAN,X.TONG,H.WU, JRNL AUTH 2 G.LI,C.CAO JRNL TITL STRUCTURAL BASIS FOR SITE-SPECIFIC READING OF UNMODIFIED R2 JRNL TITL 2 OF HISTONE H3 TAIL BY UHRF1 PHD FINGER. JRNL REF CELL RES. V. 21 1379 2011 JRNL REFN ISSN 1001-0602 JRNL PMID 21808299 JRNL DOI 10.1038/CR.2011.123 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.19 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LGK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000102366. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.13 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM [U-100% 13C; U-100% 15N] REMARK 210 ENTITY_1-1, 1.8 MM ENTITY_2-2, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO; 3D HNCA; 3D REMARK 210 HN(CO)CA; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D HCCH-TOCSY; 3D HCCH-COSY; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D EDITED 15N/13C REMARK 210 NOESY; 2D 1H-1H COSY; 2D 1H-1H REMARK 210 NOESY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH 2.19, TALOS, NMRPIPE, REMARK 210 SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 LEU A 333 -78.06 -87.26 REMARK 500 1 ASP A 339 68.95 -172.77 REMARK 500 1 HIS A 354 5.24 -68.65 REMARK 500 2 CYS A 334 -40.94 77.66 REMARK 500 2 HIS A 354 2.17 -69.05 REMARK 500 3 LEU A 333 -78.46 -84.57 REMARK 500 3 GLN A 338 50.97 30.69 REMARK 500 3 ASP A 339 79.45 73.02 REMARK 500 3 PRO A 360 109.33 -57.01 REMARK 500 3 M3L B 9 46.67 -72.44 REMARK 500 4 LEU A 333 -93.89 -84.87 REMARK 500 4 ASP A 339 71.98 -159.34 REMARK 500 4 HIS A 354 8.65 -62.07 REMARK 500 4 PRO A 360 109.87 -57.78 REMARK 500 5 HIS A 354 5.34 -61.62 REMARK 500 5 M3L B 9 55.98 -96.54 REMARK 500 6 ASP A 339 69.19 -165.84 REMARK 500 6 HIS A 354 7.34 -68.36 REMARK 500 6 THR B 3 128.90 60.19 REMARK 500 7 LEU A 333 -77.28 -95.95 REMARK 500 7 HIS A 354 2.22 -69.13 REMARK 500 7 ILE A 355 -19.75 -45.69 REMARK 500 7 ASN A 378 6.65 50.05 REMARK 500 7 ARG B 2 112.78 55.94 REMARK 500 8 CYS A 329 69.95 -111.77 REMARK 500 8 ARG A 337 93.38 52.53 REMARK 500 8 HIS A 354 9.09 -68.91 REMARK 500 8 ILE A 355 -18.99 -48.95 REMARK 500 8 PRO A 360 109.98 -56.53 REMARK 500 8 M3L B 9 -176.44 -63.63 REMARK 500 9 LEU A 333 -91.94 -88.50 REMARK 500 9 ARG A 337 47.61 -140.21 REMARK 500 9 ASP A 339 69.40 -159.21 REMARK 500 9 HIS A 354 5.34 -68.43 REMARK 500 9 PRO A 360 109.76 -56.25 REMARK 500 10 CYS A 334 -42.38 79.07 REMARK 500 10 ARG A 337 87.85 -150.24 REMARK 500 10 HIS A 354 9.02 -69.79 REMARK 500 10 M3L B 9 -89.45 -50.04 REMARK 500 11 CYS A 329 68.79 -107.80 REMARK 500 11 ASP A 339 72.89 43.07 REMARK 500 11 HIS A 354 3.28 -66.75 REMARK 500 11 ALA B 7 -154.09 51.09 REMARK 500 12 LEU A 333 -95.90 -89.48 REMARK 500 12 GLN A 338 45.83 35.14 REMARK 500 12 ASP A 339 82.68 77.10 REMARK 500 13 CYS A 334 -41.75 73.62 REMARK 500 13 ASP A 339 65.08 37.94 REMARK 500 13 HIS A 354 9.47 -68.83 REMARK 500 14 ASP A 321 66.30 -117.31 REMARK 500 REMARK 500 THIS ENTRY HAS 78 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 380 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 315 SG REMARK 620 2 CYS A 318 SG 107.4 REMARK 620 3 CYS A 326 SG 112.3 111.2 REMARK 620 4 CYS A 329 SG 109.3 109.7 107.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 381 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 331 SG REMARK 620 2 CYS A 334 SG 104.7 REMARK 620 3 HIS A 354 NE2 110.6 108.6 REMARK 620 4 CYS A 357 SG 110.0 111.0 111.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 382 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 346 SG REMARK 620 2 CYS A 349 SG 112.2 REMARK 620 3 CYS A 373 SG 115.2 109.5 REMARK 620 4 CYS A 376 SG 107.8 104.8 106.6 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 380 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 381 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 382 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17812 RELATED DB: BMRB REMARK 900 RELATED ID: 2LGG RELATED DB: PDB REMARK 900 RELATED ID: 2LGL RELATED DB: PDB DBREF 2LGK A 311 379 UNP Q96T88 UHRF1_HUMAN 298 366 DBREF 2LGK B 1 12 PDB 2LGK 2LGK 1 12 SEQRES 1 A 69 SER GLY PRO SER CYS LYS HIS CYS LYS ASP ASP VAL ASN SEQRES 2 A 69 ARG LEU CYS ARG VAL CYS ALA CYS HIS LEU CYS GLY GLY SEQRES 3 A 69 ARG GLN ASP PRO ASP LYS GLN LEU MET CYS ASP GLU CYS SEQRES 4 A 69 ASP MET ALA PHE HIS ILE TYR CYS LEU ASP PRO PRO LEU SEQRES 5 A 69 SER SER VAL PRO SER GLU ASP GLU TRP TYR CYS PRO GLU SEQRES 6 A 69 CYS ARG ASN ASP SEQRES 1 B 12 ALA ARG THR LYS GLN THR ALA ARG M3L SER THR GLY MODRES 2LGK M3L B 9 LYS N-TRIMETHYLLYSINE HET M3L B 9 31 HET ZN A 380 1 HET ZN A 381 1 HET ZN A 382 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 ZN 3(ZN 2+) HELIX 1 1 ASP A 339 GLN A 343 5 5 HELIX 2 2 CYS A 373 ASN A 378 1 6 SHEET 1 A 2 MET A 345 CYS A 346 0 SHEET 2 A 2 MET A 351 ALA A 352 -1 O MET A 351 N CYS A 346 LINK C ARG B 8 N M3L B 9 1555 1555 1.30 LINK C M3L B 9 N SER B 10 1555 1555 1.31 LINK SG CYS A 315 ZN ZN A 380 1555 1555 2.30 LINK SG CYS A 318 ZN ZN A 380 1555 1555 2.30 LINK SG CYS A 326 ZN ZN A 380 1555 1555 2.30 LINK SG CYS A 329 ZN ZN A 380 1555 1555 2.30 LINK SG CYS A 331 ZN ZN A 381 1555 1555 2.30 LINK SG CYS A 334 ZN ZN A 381 1555 1555 2.30 LINK SG CYS A 346 ZN ZN A 382 1555 1555 2.31 LINK SG CYS A 349 ZN ZN A 382 1555 1555 2.31 LINK NE2 HIS A 354 ZN ZN A 381 1555 1555 2.00 LINK SG CYS A 357 ZN ZN A 381 1555 1555 2.31 LINK SG CYS A 373 ZN ZN A 382 1555 1555 2.31 LINK SG CYS A 376 ZN ZN A 382 1555 1555 2.30 SITE 1 AC1 4 CYS A 315 CYS A 318 CYS A 326 CYS A 329 SITE 1 AC2 4 CYS A 331 CYS A 334 HIS A 354 CYS A 357 SITE 1 AC3 4 CYS A 346 CYS A 349 CYS A 373 CYS A 376 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