HEADER METAL BINDING PROTEIN 27-MAY-24 9C0O TITLE CRYSTAL STRUCTURE OF DMCFP1 PHD FINGER BOUND TO H3K4ME3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CXXC-TYPE ZINC FINGER PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHD FINGER AND CXXC DOMAIN-CONTAINING PROTEIN 1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE H3.3C; COMPND 8 CHAIN: D; COMPND 9 SYNONYM: HISTONE H3.5; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: CFP1, CG17446; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS CHROMATIN BINDING PROTEIN, HISTONE H3 READER, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.GREGOIRE,J.F.COUTURE REVDAT 1 03-JUL-24 9C0O 0 JRNL AUTH S.GREGOIRE,J.GREGOIRE,Y.YANG,S.CAPITANI,M.JOSHI,S.SARVAN, JRNL AUTH 2 A.ZAKER,Z.NING,D.FIGEYS,K.ULRICH,J.S.BRUNZELLE,A.MER, JRNL AUTH 3 J.F.COUTURE JRNL TITL STRUCTURAL INSIGHTS INTO AN ATYPICAL HISTONE BINDING JRNL TITL 2 MECHANISM BY A PHD FINGER. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.AFONINE,R.W.GROSSE-KUNSTLEVE,N.ECHOLS,J.J.HEADD, REMARK 1 AUTH 2 N.W.MORIARTY,M.MUSTYAKIMOV,T.C.TERWILLIGER,A.URZHUMTSEV, REMARK 1 AUTH 3 P.H.ZWART,P.D.ADAMS REMARK 1 TITL TOWARDS AUTOMATED CRYSTALLOGRAPHIC STRUCTURE REFINEMENT WITH REMARK 1 TITL 2 PHENIX.REFINE. REMARK 1 REF ACTA CRYSTALLOGR D BIOL V. 68 352 2012 REMARK 1 REF 2 CRYSTALLOGR REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 22505256 REMARK 1 DOI 10.1107/S0907444912001308 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 10746 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 548 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 31.9500 - 2.4300 1.00 2660 154 0.1523 0.1716 REMARK 3 2 2.4300 - 1.9300 1.00 2567 126 0.1547 0.2126 REMARK 3 3 1.9300 - 1.6800 0.99 2493 141 0.1607 0.2234 REMARK 3 4 1.6800 - 1.5300 0.99 2478 127 0.1775 0.2518 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.146 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.498 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.29 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 : 0.004 648 REMARK 3 ANGLE : 0.713 873 REMARK 3 CHIRALITY : 0.049 84 REMARK 3 PLANARITY : 0.005 115 REMARK 3 DIHEDRAL : 6.039 94 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 9C0O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1000284500. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-24 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 : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10748 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 31.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.13400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 13.60 REMARK 200 R MERGE FOR SHELL (I) : 1.37200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG3350, 0.01M TRIS PH8.5, 0.2M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 16.63500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.78000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.56000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.78000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.63500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.56000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 GLY A 54 REMARK 465 GLY A 55 REMARK 465 LYS A 56 REMARK 465 SER D 10 REMARK 465 THR D 11 REMARK 465 GLY D 12 REMARK 465 GLY D 13 REMARK 465 LYS D 14 REMARK 465 TYR D 15 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 ASP A 69 CG OD1 OD2 REMARK 470 THR D 6 OG1 CG2 REMARK 470 ARG D 8 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 9 CG CD CE NZ 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 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 58 OE1 REMARK 620 2 GLU A 58 OE2 55.0 REMARK 620 3 HIS A 98 ND1 83.0 31.3 REMARK 620 4 ARG A 119 OXT 76.6 24.4 6.9 REMARK 620 5 HOH A 309 O 81.3 28.3 4.3 4.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 65 SG REMARK 620 2 CYS A 70 SG 118.1 REMARK 620 3 HIS A 85 NE2 109.0 117.8 REMARK 620 4 HOH A 332 O 107.8 108.5 92.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 77 SG REMARK 620 2 CYS A 80 SG 107.4 REMARK 620 3 CYS A 104 SG 110.7 113.7 REMARK 620 4 CYS A 107 SG 106.9 111.0 107.0 REMARK 620 N 1 2 3 DBREF 9C0O A 56 119 UNP Q9W352 CXXC1_DROME 56 119 DBREF 9C0O D 1 15 UNP Q6NXT2 H3C_HUMAN 2 16 SEQADV 9C0O GLY A 54 UNP Q9W352 EXPRESSION TAG SEQADV 9C0O GLY A 55 UNP Q9W352 EXPRESSION TAG SEQADV 9C0O TYR D 15 UNP Q6NXT2 ALA 16 CONFLICT SEQRES 1 A 66 GLY GLY LYS GLN GLU ASP GLN ALA TYR CYS ILE CYS ARG SEQRES 2 A 66 SER SER ASP CYS SER ARG PHE MET ILE GLY CYS ASP GLY SEQRES 3 A 66 CYS GLU GLU TRP TYR HIS GLY ASP CYS ILE GLY ILE THR SEQRES 4 A 66 GLU LYS GLU ALA LYS HIS ILE LYS GLN TYR TYR CYS ARG SEQRES 5 A 66 ARG CYS LYS LYS GLU ASN PRO GLU LEU GLN THR ILE PHE SEQRES 6 A 66 ARG SEQRES 1 D 15 ALA ARG THR M3L GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 D 15 LYS TYR MODRES 9C0O M3L D 4 LYS MODIFIED RESIDUE HET M3L D 4 12 HET DMS A 201 4 HET ZN A 202 1 HET ZN A 203 1 HET ZN A 204 1 HET SO4 A 205 5 HET SO4 A 206 5 HETNAM M3L N-TRIMETHYLLYSINE HETNAM DMS DIMETHYL SULFOXIDE HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 DMS C2 H6 O S FORMUL 4 ZN 3(ZN 2+) FORMUL 7 SO4 2(O4 S 2-) FORMUL 9 HOH *70(H2 O) HELIX 1 AA1 GLN A 60 TYR A 62 5 3 HELIX 2 AA2 THR A 92 LYS A 97 1 6 HELIX 3 AA3 CYS A 104 ASN A 111 1 8 SHEET 1 AA1 4 ILE A 64 CYS A 65 0 SHEET 2 AA1 4 TRP A 83 HIS A 85 -1 O TRP A 83 N CYS A 65 SHEET 3 AA1 4 MET A 74 GLY A 76 -1 N ILE A 75 O TYR A 84 SHEET 4 AA1 4 THR D 3 M3L D 4 -1 O M3L D 4 N MET A 74 SHEET 1 AA2 2 ILE A 99 GLN A 101 0 SHEET 2 AA2 2 ILE A 117 PHE A 118 -1 O ILE A 117 N GLN A 101 SSBOND 1 CYS A 63 CYS A 88 1555 1555 2.03 LINK C THR D 3 N M3L D 4 1555 1555 1.32 LINK C M3L D 4 N AGLN D 5 1555 1555 1.33 LINK C M3L D 4 N BGLN D 5 1555 1555 1.33 LINK OE1 GLU A 58 ZN ZN A 204 1555 4555 2.21 LINK OE2 GLU A 58 ZN ZN A 204 1555 4555 2.50 LINK SG CYS A 65 ZN ZN A 202 1555 1555 2.27 LINK SG CYS A 70 ZN ZN A 202 1555 1555 2.26 LINK SG CYS A 77 ZN ZN A 203 1555 1555 2.32 LINK SG CYS A 80 ZN ZN A 203 1555 1555 2.35 LINK NE2 HIS A 85 ZN ZN A 202 1555 1555 2.21 LINK ND1 HIS A 98 ZN ZN A 204 1555 1555 2.27 LINK SG CYS A 104 ZN ZN A 203 1555 1555 2.33 LINK SG CYS A 107 ZN ZN A 203 1555 1555 2.31 LINK OXT ARG A 119 ZN ZN A 204 1555 1555 1.92 LINK ZN ZN A 202 O HOH A 332 1555 4555 2.09 LINK ZN ZN A 204 O HOH A 309 1555 3555 2.02 CRYST1 33.270 43.120 47.560 90.00 90.00 90.00 P 21 21 21 4 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 0.030057 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023191 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021026 0.00000