PDB Short entry for 2LQ6 HEADER METAL BINDING PROTEIN 25-FEB-12 2LQ6 TITLE SOLUTION STRUCTURE OF BRD1 PHD2 FINGER COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 317-394; COMPND 5 SYNONYM: BR140-LIKE PROTEIN, BROMODOMAIN AND PHD FINGER-CONTAINING COMPND 6 PROTEIN 2; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BRD1, BRL, BRPF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28 KEYWDS PHD FINGER, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 MDLTYP MINIMIZED AVERAGE AUTHOR L.LIU,J.WU REVDAT 1 24-OCT-12 2LQ6 0 JRNL AUTH L.LIU,S.QIN,J.ZHANG,P.JI,Y.SHI,J.WU JRNL TITL SOLUTION STRUCTURE OF AN ATYPICAL PHD FINGER IN BRPF2 AND JRNL TITL 2 ITS INTERACTION WITH DNA JRNL REF J.STRUCT.BIOL. V. 180 165 2012 JRNL REFN ISSN 1047-8477 JRNL PMID 22820306 JRNL DOI 10.1016/J.JSB.2012.06.014 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LQ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAR-12. REMARK 100 THE RCSB ID CODE IS RCSB102694. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM [U-15N] PROTEIN-1, 90% REMARK 210 H2O/10% D2O; 0.4 MM [U-13C; U- REMARK 210 15N] PROTEIN-2, 90% H2O/10% D2O; REMARK 210 0.4 MM [U-13C; U-15N] PROTEIN-3, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D HNCO; 3D HN(CO)CA; REMARK 210 3D HBHA(CO)NH; 3D H(CCO)NH; 3D REMARK 210 HCCH-COSY; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C 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 : CNS 1.2, SPARKY, NMRPIPE REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 308 REMARK 465 GLY A 309 REMARK 465 HIS A 310 REMARK 465 HIS A 311 REMARK 465 HIS A 312 REMARK 465 HIS A 313 REMARK 465 HIS A 314 REMARK 465 HIS A 315 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 HZ1 LYS A 363 OE2 GLU A 365 1.59 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 LYS A 324 107.35 -53.33 REMARK 500 1 CYS A 330 -50.60 168.50 REMARK 500 1 GLN A 332 -154.64 -133.12 REMARK 500 1 LYS A 333 -64.96 -134.61 REMARK 500 1 VAL A 335 -30.33 176.28 REMARK 500 1 LYS A 343 106.40 79.27 REMARK 500 1 CYS A 346 -63.95 -125.63 REMARK 500 1 TYR A 347 79.11 45.24 REMARK 500 2 ASN A 317 -61.12 -170.69 REMARK 500 2 PRO A 320 88.71 -64.45 REMARK 500 2 ALA A 321 17.84 -141.85 REMARK 500 2 LYS A 324 84.99 -66.08 REMARK 500 2 CYS A 330 -3.80 -152.89 REMARK 500 2 LYS A 333 -74.66 -54.83 REMARK 500 2 VAL A 335 -32.23 -137.77 REMARK 500 2 HIS A 342 -66.45 -167.91 REMARK 500 2 LYS A 343 -74.90 66.39 REMARK 500 2 CYS A 346 -44.74 -173.92 REMARK 500 2 SER A 393 39.97 -172.31 REMARK 500 3 PRO A 319 100.36 -24.87 REMARK 500 3 PRO A 320 37.94 -79.76 REMARK 500 3 ALA A 321 10.13 -153.49 REMARK 500 3 ARG A 322 29.15 -146.02 REMARK 500 3 LYS A 324 64.72 -67.10 REMARK 500 3 CYS A 330 175.84 166.80 REMARK 500 3 VAL A 335 -54.11 74.58 REMARK 500 3 LYS A 343 118.84 74.42 REMARK 500 3 CYS A 346 -75.75 -107.18 REMARK 500 3 TYR A 347 75.16 46.83 REMARK 500 3 PRO A 391 -160.69 -62.70 REMARK 500 4 ALA A 321 27.05 -156.24 REMARK 500 4 CYS A 330 -16.93 -173.22 REMARK 500 4 LYS A 331 31.34 72.06 REMARK 500 4 LYS A 333 -81.32 -51.99 REMARK 500 4 HIS A 342 -78.02 -151.48 REMARK 500 4 LYS A 343 -61.51 70.06 REMARK 500 4 ALA A 344 -72.23 -156.87 REMARK 500 4 CYS A 346 144.54 -174.73 REMARK 500 4 LEU A 370 -34.22 -157.26 REMARK 500 4 PRO A 390 98.26 -26.39 REMARK 500 4 SER A 393 -151.91 -126.54 REMARK 500 5 CYS A 330 -32.71 135.65 REMARK 500 5 LYS A 331 33.75 71.16 REMARK 500 5 LYS A 333 -118.88 50.96 REMARK 500 5 HIS A 342 -159.96 -92.70 REMARK 500 5 LYS A 343 121.82 77.06 REMARK 500 5 ASN A 345 64.51 -110.13 REMARK 500 5 CYS A 346 -74.18 -172.38 REMARK 500 5 TYR A 347 79.01 45.53 REMARK 500 5 PRO A 391 106.01 -49.96 REMARK 500 REMARK 500 THIS ENTRY HAS 206 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 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 348 OG1 REMARK 620 2 CYS A 346 SG 88.1 REMARK 620 3 CYS A 385 SG 93.1 159.8 REMARK 620 4 HIS A 388 ND1 171.3 89.2 92.2 REMARK 620 5 CYS A 341 SG 85.6 100.5 99.7 86.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 329 O REMARK 620 2 CYS A 330 SG 76.6 REMARK 620 3 CYS A 354 SG 90.0 152.2 REMARK 620 4 HIS A 351 ND1 152.1 89.6 111.8 REMARK 620 5 CYS A 327 SG 77.2 101.1 99.6 81.9 REMARK 620 N 1 2 3 4 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18296 RELATED DB: BMRB DBREF 2LQ6 A 317 394 UNP O95696 BRD1_HUMAN 317 394 SEQADV 2LQ6 MET A 308 UNP O95696 EXPRESSION TAG SEQADV 2LQ6 GLY A 309 UNP O95696 EXPRESSION TAG SEQADV 2LQ6 HIS A 310 UNP O95696 EXPRESSION TAG SEQADV 2LQ6 HIS A 311 UNP O95696 EXPRESSION TAG SEQADV 2LQ6 HIS A 312 UNP O95696 EXPRESSION TAG SEQADV 2LQ6 HIS A 313 UNP O95696 EXPRESSION TAG SEQADV 2LQ6 HIS A 314 UNP O95696 EXPRESSION TAG SEQADV 2LQ6 HIS A 315 UNP O95696 EXPRESSION TAG SEQADV 2LQ6 MET A 316 UNP O95696 EXPRESSION TAG SEQADV 2LQ6 SER A 338 UNP O95696 CYS 338 ENGINEERED MUTATION SEQADV 2LQ6 SER A 393 UNP O95696 CYS 393 ENGINEERED MUTATION SEQRES 1 A 87 MET GLY HIS HIS HIS HIS HIS HIS MET ASN ILE PRO PRO SEQRES 2 A 87 ALA ARG TRP LYS LEU THR CYS TYR LEU CYS LYS GLN LYS SEQRES 3 A 87 GLY VAL GLY ALA SER ILE GLN CYS HIS LYS ALA ASN CYS SEQRES 4 A 87 TYR THR ALA PHE HIS VAL THR CYS ALA GLN LYS ALA GLY SEQRES 5 A 87 LEU TYR MET LYS MET GLU PRO VAL LYS GLU LEU THR GLY SEQRES 6 A 87 GLY GLY THR THR PHE SER VAL ARG LYS THR ALA TYR CYS SEQRES 7 A 87 ASP VAL HIS THR PRO PRO GLY SER THR HET ZN A 401 1 HET ZN A 402 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 VAL A 352 GLY A 359 1 8 HELIX 2 2 CYS A 385 THR A 389 5 5 SHEET 1 A 2 SER A 338 GLN A 340 0 SHEET 2 A 2 ALA A 349 HIS A 351 -1 O PHE A 350 N ILE A 339 SHEET 1 B 2 MET A 362 GLU A 369 0 SHEET 2 B 2 THR A 376 ALA A 383 -1 O THR A 382 N LYS A 363 LINK OG1 THR A 348 ZN ZN A 402 1555 1555 1.76 LINK O LEU A 329 ZN ZN A 401 1555 1555 2.13 LINK SG CYS A 346 ZN ZN A 402 1555 1555 2.17 LINK SG CYS A 330 ZN ZN A 401 1555 1555 2.18 LINK SG CYS A 385 ZN ZN A 402 1555 1555 2.18 LINK SG CYS A 354 ZN ZN A 401 1555 1555 2.20 LINK ND1 HIS A 351 ZN ZN A 401 1555 1555 2.24 LINK ND1 HIS A 388 ZN ZN A 402 1555 1555 2.24 LINK SG CYS A 341 ZN ZN A 402 1555 1555 2.45 LINK SG CYS A 327 ZN ZN A 401 1555 1555 2.46 SITE 1 AC1 5 CYS A 327 LEU A 329 CYS A 330 HIS A 351 SITE 2 AC1 5 CYS A 354 SITE 1 AC2 5 CYS A 341 CYS A 346 THR A 348 CYS A 385 SITE 2 AC2 5 HIS A 388 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