HEADER TRANSCRIPTION 09-SEP-16 5TAB TITLE CRYSTAL STRUCTURE OF THE PHD FINGER OF PHF20 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHD FINGER PROTEIN 20; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 651-698; COMPND 5 SYNONYM: GLIOMA-EXPRESSED ANTIGEN 2,HEPATOCELLULAR CARCINOMA- COMPND 6 ASSOCIATED ANTIGEN 58,NOVEL ZINC FINGER PROTEIN,TRANSCRIPTION FACTOR COMPND 7 TZP; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PHF20, C20ORF104, GLEA2, HCA58, NZF, TZP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: RIPL KEYWDS PHD FINGER, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR B.J.KLEIN,T.G.KUTATELADZE REVDAT 5 06-MAR-24 5TAB 1 REMARK REVDAT 4 25-DEC-19 5TAB 1 REMARK REVDAT 3 16-MAY-18 5TAB 1 JRNL REVDAT 2 20-SEP-17 5TAB 1 REMARK REVDAT 1 26-OCT-16 5TAB 0 JRNL AUTH B.J.KLEIN,X.WANG,G.CUI,C.YUAN,M.V.BOTUYAN,K.LIN,Y.LU,X.WANG, JRNL AUTH 2 Y.ZHAO,C.J.BRUNS,G.MER,X.SHI,T.G.KUTATELADZE JRNL TITL PHF20 READERS LINK METHYLATION OF HISTONE H3K4 AND P53 WITH JRNL TITL 2 H4K16 ACETYLATION. JRNL REF CELL REP V. 17 1158 2016 JRNL REFN ESSN 2211-1247 JRNL PMID 27760318 JRNL DOI 10.1016/J.CELREP.2016.09.056 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 17326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.121 REMARK 3 R VALUE (WORKING SET) : 0.118 REMARK 3 FREE R VALUE : 0.144 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.470 REMARK 3 FREE R VALUE TEST SET COUNT : 1641 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 31.6979 - 2.8612 1.00 1358 143 0.1211 0.1385 REMARK 3 2 2.8612 - 2.2712 1.00 1333 139 0.1300 0.1573 REMARK 3 3 2.2712 - 1.9842 1.00 1334 136 0.1234 0.1471 REMARK 3 4 1.9842 - 1.8028 1.00 1295 142 0.1115 0.1346 REMARK 3 5 1.8028 - 1.6736 1.00 1327 136 0.0970 0.1233 REMARK 3 6 1.6736 - 1.5749 1.00 1321 137 0.0949 0.1231 REMARK 3 7 1.5749 - 1.4960 1.00 1311 137 0.0923 0.1158 REMARK 3 8 1.4960 - 1.4309 0.99 1320 142 0.0968 0.1284 REMARK 3 9 1.4309 - 1.3758 0.99 1282 131 0.1083 0.1426 REMARK 3 10 1.3758 - 1.3284 0.98 1278 135 0.1286 0.1560 REMARK 3 11 1.3284 - 1.2868 0.97 1280 133 0.1561 0.2048 REMARK 3 12 1.2868 - 1.2500 0.94 1246 130 0.1752 0.2167 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.012 443 REMARK 3 ANGLE : 1.472 597 REMARK 3 CHIRALITY : 0.076 63 REMARK 3 PLANARITY : 0.009 79 REMARK 3 DIHEDRAL : 17.959 166 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 5TAB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000223952. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33909 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 31.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANOL PH 6.5, 2.55 M REMARK 280 AMMONIUM SULFATE TITRATED WITH 0.006 ML PER 1 ML 1 N HCL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.97600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.95200 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 25.46400 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.44000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 8.48800 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: 230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 ASN A 18 -149.59 -122.33 REMARK 500 PHE A 20 88.85 -150.95 REMARK 500 GLU A 26 -61.05 -91.17 REMARK 500 LYS A 46 51.91 -95.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 271 DISTANCE = 6.80 ANGSTROMS 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 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 10 SG REMARK 620 2 CYS A 12 SG 114.9 REMARK 620 3 HIS A 32 ND1 103.5 99.2 REMARK 620 4 CYS A 35 SG 109.0 114.3 115.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 CYS A 27 SG 105.1 REMARK 620 3 CYS A 49 SG 111.1 112.8 REMARK 620 4 CYS A 52 SG 112.3 107.5 108.0 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 103 DBREF 5TAB A 6 53 UNP Q9BVI0 PHF20_HUMAN 651 698 SEQADV 5TAB GLY A 1 UNP Q9BVI0 EXPRESSION TAG SEQADV 5TAB PRO A 2 UNP Q9BVI0 EXPRESSION TAG SEQADV 5TAB LEU A 3 UNP Q9BVI0 EXPRESSION TAG SEQADV 5TAB GLY A 4 UNP Q9BVI0 EXPRESSION TAG SEQADV 5TAB SER A 5 UNP Q9BVI0 EXPRESSION TAG SEQADV 5TAB SER A 29 UNP Q9BVI0 CYS 674 ENGINEERED MUTATION SEQRES 1 A 53 GLY PRO LEU GLY SER GLU VAL VAL ARG CYS ILE CYS GLU SEQRES 2 A 53 VAL GLN GLU GLU ASN ASP PHE MET ILE GLN CYS GLU GLU SEQRES 3 A 53 CYS GLN SER TRP GLN HIS GLY VAL CYS MET GLY LEU LEU SEQRES 4 A 53 GLU GLU ASN VAL PRO GLU LYS TYR THR CYS TYR VAL CYS SEQRES 5 A 53 GLN HET ZN A 101 1 HET ZN A 102 1 HET GOL A 103 28 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *71(H2 O) HELIX 1 AA1 GLY A 1 SER A 5 5 5 SHEET 1 AA1 2 MET A 21 GLN A 23 0 SHEET 2 AA1 2 TRP A 30 HIS A 32 -1 O GLN A 31 N ILE A 22 LINK SG CYS A 10 ZN ZN A 102 1555 1555 2.34 LINK SG CYS A 12 ZN ZN A 102 1555 1555 2.29 LINK SG CYS A 24 ZN ZN A 101 1555 1555 2.35 LINK SG CYS A 27 ZN ZN A 101 1555 1555 2.35 LINK ND1 HIS A 32 ZN ZN A 102 1555 1555 2.08 LINK SG CYS A 35 ZN ZN A 102 1555 1555 2.31 LINK SG CYS A 49 ZN ZN A 101 1555 1555 2.33 LINK SG CYS A 52 ZN ZN A 101 1555 1555 2.33 SITE 1 AC1 4 CYS A 24 CYS A 27 CYS A 49 CYS A 52 SITE 1 AC2 4 CYS A 10 CYS A 12 HIS A 32 CYS A 35 SITE 1 AC3 7 SER A 5 GLU A 6 ARG A 9 CYS A 27 SITE 2 AC3 7 SER A 29 GLU A 45 HOH A 223 CRYST1 46.739 46.739 50.928 90.00 90.00 120.00 P 61 6 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 0.021395 0.012353 0.000000 0.00000 SCALE2 0.000000 0.024705 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019636 0.00000