HEADER PEPTIDE BINDING PROTEIN 09-JAN-20 6VHF TITLE CRYSTAL STRUCTURE OF RBBP5 INTERACTING DOMAIN OF CFP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHD-TYPE DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS SOURCE 3 144.50 / IMI 039719); SOURCE 4 ORGANISM_TAXID: 759272; SOURCE 5 STRAIN: DSM 1495 / CBS 144.50 / IMI 039719; SOURCE 6 GENE: CTHT_0014220; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE, MLL, CFP1, RBBP5, COMPASS, EPIGENETICS, PEPTIDE BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.JOSHI,J.F.COUTURE REVDAT 3 03-APR-24 6VHF 1 REMARK REVDAT 2 06-MAR-24 6VHF 1 REMARK REVDAT 1 22-JAN-20 6VHF 0 JRNL AUTH Y.YANG,M.JOSHI,Y.H.TAKAHASHI,Z.NING,Q.QU,J.S.BRUNZELLE, JRNL AUTH 2 G.SKINIOTIS,D.FIGEYS,A.SHILATIFARD,J.F.COUTURE JRNL TITL A NON-CANONICAL MONOVALENT ZINC FINGER STABILIZES THE JRNL TITL 2 INTEGRATION OF CFP1 INTO THE H3K4 METHYLTRANSFERASE COMPLEX JRNL TITL 3 COMPASS. JRNL REF NUCLEIC ACIDS RES. V. 48 421 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 31724694 JRNL DOI 10.1093/NAR/GKZ1037 REMARK 2 REMARK 2 RESOLUTION. 2.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 8459 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 422 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 49.0290 - 3.3321 1.00 2736 198 0.2257 0.2650 REMARK 3 2 3.3321 - 2.4490 0.99 2666 124 0.2423 0.2913 REMARK 3 3 2.4490 - 2.3110 0.98 2635 100 0.2515 0.3003 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1087 REMARK 3 ANGLE : 0.904 1463 REMARK 3 CHIRALITY : 0.041 168 REMARK 3 PLANARITY : 0.006 192 REMARK 3 DIHEDRAL : 21.498 677 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6VHF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000246400. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8459 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.310 REMARK 200 RESOLUTION RANGE LOW (A) : 51.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37700 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PRELIMINARY INCOMPLETE MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NH4CL, AND 22% (W/V) PEG 3350, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.63300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.80700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.06600 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.63300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.80700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.06600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.63300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.80700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.06600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.63300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.80700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 39.06600 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ILE A 405 REMARK 465 PHE A 406 REMARK 465 SER A 407 REMARK 465 THR A 408 REMARK 465 ARG A 409 REMARK 465 SER A 410 REMARK 465 LEU A 411 REMARK 465 ASP A 412 REMARK 465 ASN A 413 REMARK 465 PRO A 414 REMARK 465 PRO A 415 REMARK 465 TYR A 416 REMARK 465 VAL A 417 REMARK 465 THR A 418 REMARK 465 THR A 419 REMARK 465 THR A 420 REMARK 465 ILE A 421 REMARK 465 LYS A 422 REMARK 465 ASN A 423 REMARK 465 PRO A 424 REMARK 465 GLU A 425 REMARK 465 ASP A 426 REMARK 465 ASP A 427 REMARK 465 THR A 428 REMARK 465 PRO A 429 REMARK 465 ALA A 430 REMARK 465 ALA A 431 REMARK 465 THR A 432 REMARK 465 SER A 433 REMARK 465 SER A 434 REMARK 465 ASN A 435 REMARK 465 SER A 436 REMARK 465 ALA A 437 REMARK 465 GLU A 438 REMARK 465 THR A 439 REMARK 465 ALA A 440 REMARK 465 ALA A 441 REMARK 465 GLY A 442 REMARK 465 MET A 500 REMARK 465 ARG A 501 REMARK 465 ARG A 502 REMARK 465 MET A 503 REMARK 465 LYS A 504 REMARK 465 GLU A 505 REMARK 465 ARG A 506 REMARK 465 ASN A 507 REMARK 465 GLU A 508 REMARK 465 VAL A 509 REMARK 465 ILE A 510 REMARK 465 ALA A 511 REMARK 465 ILE A 512 REMARK 465 GLU A 513 REMARK 465 GLU A 514 REMARK 465 ASP A 515 REMARK 465 GLU A 516 REMARK 465 ASP A 517 REMARK 465 ASP A 518 REMARK 465 ASP A 519 REMARK 465 GLU A 520 REMARK 465 HIS A 521 REMARK 465 GLY A 522 REMARK 465 ASN A 523 REMARK 465 GLY A 524 REMARK 465 PHE A 525 REMARK 465 LEU A 526 REMARK 465 ARG A 527 REMARK 465 GLU A 528 REMARK 465 GLU A 529 REMARK 465 LYS A 530 REMARK 465 LEU A 531 REMARK 465 GLY A 532 REMARK 465 HIS A 533 REMARK 465 LYS A 534 REMARK 465 ARG A 535 REMARK 465 SER A 536 REMARK 465 ASP A 537 REMARK 465 GLY A 538 REMARK 465 ASP A 539 REMARK 465 ARG A 540 REMARK 465 MET A 541 REMARK 465 ASP A 542 REMARK 465 LEU A 543 REMARK 465 ASP A 544 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE A 499 CG CD1 CD2 CE1 CE2 CZ 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 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 378 SG REMARK 620 2 CYS A 451 SG 104.6 REMARK 620 3 CYS A 456 SG 105.8 121.7 REMARK 620 4 HIS A 459 ND1 105.4 100.3 117.5 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 601 DBREF 6VHF A 322 544 UNP G0S1N3 G0S1N3_CHATD 322 544 SEQRES 1 A 223 ALA LEU THR PRO GLU GLU TYR ALA GLU LEU THR ALA SER SEQRES 2 A 223 ALA GLU THR ARG SER LYS LEU SER GLU GLN ILE ALA LEU SEQRES 3 A 223 CYS ARG GLN MET LEU GLN LEU ILE GLU LEU ALA ILE ALA SEQRES 4 A 223 ARG ARG GLU ALA ALA ILE ALA ALA GLY ILE PRO GLY ILE SEQRES 5 A 223 THR LYS ASP ILE CYS GLY TYR ASP THR ARG LEU ASP THR SEQRES 6 A 223 VAL GLY ALA ALA HIS GLN PHE SER LEU PHE LEU GLN SER SEQRES 7 A 223 PRO GLN GLY GLN SER ILE PHE SER THR ARG SER LEU ASP SEQRES 8 A 223 ASN PRO PRO TYR VAL THR THR THR ILE LYS ASN PRO GLU SEQRES 9 A 223 ASP ASP THR PRO ALA ALA THR SER SER ASN SER ALA GLU SEQRES 10 A 223 THR ALA ALA GLY GLN ASP PRO ARG THR ALA GLY MET CYS SEQRES 11 A 223 LEU ARG LYS LYS CYS LYS PRO HIS ASN GLY TRP GLY ALA SEQRES 12 A 223 LEU LEU THR LYS THR VAL ARG HIS ASP ILE ARG GLU LEU SEQRES 13 A 223 ALA LEU GLN ILE ARG GLU LEU LEU GLU ALA GLU GLN ARG SEQRES 14 A 223 VAL ARG ASP GLY ALA ALA GLY ARG PHE MET ARG ARG MET SEQRES 15 A 223 LYS GLU ARG ASN GLU VAL ILE ALA ILE GLU GLU ASP GLU SEQRES 16 A 223 ASP ASP ASP GLU HIS GLY ASN GLY PHE LEU ARG GLU GLU SEQRES 17 A 223 LYS LEU GLY HIS LYS ARG SER ASP GLY ASP ARG MET ASP SEQRES 18 A 223 LEU ASP HET ZN A 601 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *21(H2 O) HELIX 1 AA1 THR A 324 ALA A 368 1 45 HELIX 2 AA2 ASP A 381 ARG A 383 5 3 HELIX 3 AA3 LEU A 384 SER A 399 1 16 HELIX 4 AA4 GLY A 461 PHE A 499 1 39 LINK SG CYS A 378 ZN ZN A 601 1555 1555 2.42 LINK SG CYS A 451 ZN ZN A 601 1555 1555 2.61 LINK SG CYS A 456 ZN ZN A 601 1555 1555 2.35 LINK ND1 HIS A 459 ZN ZN A 601 1555 1555 2.16 SITE 1 AC1 4 CYS A 378 CYS A 451 CYS A 456 HIS A 459 CRYST1 67.266 71.614 78.132 90.00 90.00 90.00 I 2 2 2 8 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 0.014866 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013964 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012799 0.00000