HEADER TRANSCRIPTION 17-DEC-10 3Q1J TITLE CRYSTAL STRUCTURE OF TUDOR DOMAIN 1 OF HUMAN PHD FINGER PROTEIN 20 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHD FINGER PROTEIN 20; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-81; COMPND 5 SYNONYM: GLIOMA-EXPRESSED ANTIGEN 2, HEPATOCELLULAR CARCINOMA- COMPND 6 ASSOCIATED ANTIGEN 58, NOVEL ZINC FINGER PROTEIN, TRANSCRIPTION COMPND 7 FACTOR 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODON PLUS RIL (STRATAGENE); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MHL KEYWDS TUDOR DOMAIN, MBT, STRUCTURAL GENOMICS CONSORTIUM, SGC, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR W.TEMPEL,Z.LI,A.K.WERNIMONT,X.CHAO,C.BIAN,R.LAM,L.CROMBET,C.BOUNTRA, AUTHOR 2 J.WEIGELT,C.H.ARROWSMITH,A.M.EDWARDS,J.MIN,STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (SGC) REVDAT 4 13-SEP-23 3Q1J 1 REMARK REVDAT 3 08-NOV-17 3Q1J 1 REMARK REVDAT 2 09-MAY-12 3Q1J 1 JRNL VERSN REVDAT 1 09-FEB-11 3Q1J 0 JRNL AUTH M.A.ADAMS-CIOABA,Z.LI,W.TEMPEL,Y.GUO,C.BIAN,Y.LI,R.LAM,J.MIN JRNL TITL CRYSTAL STRUCTURES OF THE TUDOR DOMAINS OF HUMAN PHF20 JRNL TITL 2 REVEAL NOVEL STRUCTURAL VARIATIONS ON THE ROYAL FAMILY OF JRNL TITL 3 PROTEINS. JRNL REF FEBS LETT. V. 586 859 2012 JRNL REFN ISSN 0014-5793 JRNL PMID 22449972 JRNL DOI 10.1016/J.FEBSLET.2012.02.012 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT BUSTER 2.8.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 2804 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.670 REMARK 3 FREE R VALUE TEST SET COUNT : 131 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.63 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 807 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2372 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 762 REMARK 3 BIN R VALUE (WORKING SET) : 0.2327 REMARK 3 BIN FREE R VALUE : 0.2997 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.58 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 45 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 549 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 5 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.08940 REMARK 3 B22 (A**2) : 8.24240 REMARK 3 B33 (A**2) : 1.84700 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -14.27960 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.307 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.903 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.882 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 575 ; 2.000 ; NULL REMARK 3 BOND ANGLES : 788 ; 2.000 ; NULL REMARK 3 TORSION ANGLES : 182 ; 2.000 ; NULL REMARK 3 TRIGONAL CARBON PLANES : 14 ; 2.000 ; NULL REMARK 3 GENERAL PLANES : 85 ; 5.000 ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS : 575 ; 20.000 ; NULL REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 68 ; 5.000 ; NULL REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 632 ; 4.000 ; NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.04 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.27 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.94 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE PROGRAMS MOLREP, CHAINSAW, PHENIX, REMARK 3 REFMAC, COOT AND THE FFAS03 AND MOLPROBITY SERVERS WHERE ALSO REMARK 3 USED IN THE COURSE OF REFINEMENT REMARK 4 REMARK 4 3Q1J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000063077. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2828 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.65400 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRIES 2RHU, 2EQM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG-3350, 0.2M AMMONIUM ACETATE, REMARK 280 0.1M BIS-TRIS. PRIOR TO FREEZING, A CLUSTER OF THIN RODS WAS REMARK 280 TRANSFERRED TO A DROP OF PARATONE OIL. A FRAGMENT OF THE CLUSTER REMARK 280 WAS FROZEN IN A STREAM OF COLD NITROGEN., PH 5.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K, VAPOR DIFFUSION, REMARK 280 SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 30.24900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.53100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.24900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.53100 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 300 REMARK: BIOLOGICAL UNIT WAS NOT EXPERIMENTALLY DETERMINED. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 HIS A 4 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 9 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 24 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 ARG A 49 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 51 CG OD1 ND2 REMARK 470 GLU A 69 CG CD OE1 OE2 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 LEU A 19 -167.25 -163.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE INITIAL SEQUENCE OF THE PROTEIN HAS THE FOLLOWING SEQUENCE, REMARK 999 MHHHHHHSSRENLYFQGMTKHPPNRRGISFEVGAQLEARDRLKNWYPAH REMARK 999 IEDIDYEEGKVLIHFKRWNHRYDEWFCWDSPYLRPLEKIQLRKEGLHEE REMARK 999 AUTHORS STATE THAT THE PROTEIN WAS LIKELY DEGRADED SPONTANEOUSLY REMARK 999 PRIOR TO CRYSTALLIZATION. WITH UNCLEAR DEGRADATION SITE, THE REMARK 999 CURRENT SEQRES REPRESENTES ONLY THE PROTEIN PORTION WITH VISIBLE REMARK 999 ELECTRON DENSITY. DBREF 3Q1J A 4 69 UNP Q9BVI0 PHF20_HUMAN 4 69 SEQRES 1 A 66 HIS PRO PRO ASN ARG ARG GLY ILE SER PHE GLU VAL GLY SEQRES 2 A 66 ALA GLN LEU GLU ALA ARG ASP ARG LEU LYS ASN TRP TYR SEQRES 3 A 66 PRO ALA HIS ILE GLU ASP ILE ASP TYR GLU GLU GLY LYS SEQRES 4 A 66 VAL LEU ILE HIS PHE LYS ARG TRP ASN HIS ARG TYR ASP SEQRES 5 A 66 GLU TRP PHE CYS TRP ASP SER PRO TYR LEU ARG PRO LEU SEQRES 6 A 66 GLU HET UNX A 82 1 HETNAM UNX UNKNOWN ATOM OR ION FORMUL 2 UNX X FORMUL 3 HOH *5(H2 O) HELIX 1 1 ASN A 51 ASP A 55 5 5 SHEET 1 A 5 GLU A 56 CYS A 59 0 SHEET 2 A 5 LYS A 42 PHE A 47 -1 N ILE A 45 O GLU A 56 SHEET 3 A 5 TRP A 28 ASP A 37 -1 N ASP A 37 O LYS A 42 SHEET 4 A 5 GLN A 18 ARG A 22 -1 N LEU A 19 O ALA A 31 SHEET 5 A 5 LEU A 65 ARG A 66 -1 O ARG A 66 N GLU A 20 CRYST1 60.498 41.062 28.632 90.00 110.33 90.00 C 1 2 1 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 0.016529 0.000000 0.006124 0.00000 SCALE2 0.000000 0.024353 0.000000 0.00000 SCALE3 0.000000 0.000000 0.037246 0.00000