HEADER TRANSCRIPTION 08-JUN-11 3SD4 TITLE CRYSTAL STRUCTURE OF THE FIRST TUDOR DOMAIN OF HUMAN PHF20 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHD FINGER PROTEIN 20; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: FIRST TUDOR DOMAIN, UNP RESIDUES 4-69; 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: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 ROSETTA (PLYSS); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTEV KEYWDS TUDOR DOMAIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR G.CUI,M.V.BOTUYAN,J.R.THOMPSON,G.MER REVDAT 6 03-APR-24 3SD4 1 REMARK REVDAT 5 28-FEB-24 3SD4 1 REMARK REVDAT 4 06-NOV-19 3SD4 1 REMARK SEQADV REVDAT 3 26-SEP-12 3SD4 1 JRNL REVDAT 2 15-AUG-12 3SD4 1 JRNL VERSN REVDAT 1 22-JUN-11 3SD4 0 JRNL AUTH G.CUI,S.PARK,A.I.BADEAUX,D.KIM,J.LEE,J.R.THOMPSON,F.YAN, JRNL AUTH 2 S.KANEKO,Z.YUAN,M.V.BOTUYAN,M.T.BEDFORD,J.Q.CHENG,G.MER JRNL TITL PHF20 IS AN EFFECTOR PROTEIN OF P53 DOUBLE LYSINE JRNL TITL 2 METHYLATION THAT STABILIZES AND ACTIVATES P53. JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 916 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 22864287 JRNL DOI 10.1038/NSMB.2353 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 11693 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 558 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 30.3843 - 3.0595 0.99 2876 136 0.2127 0.2172 REMARK 3 2 3.0595 - 2.4287 0.99 2779 152 0.2363 0.2159 REMARK 3 3 2.4287 - 2.1218 0.97 2751 135 0.2440 0.2977 REMARK 3 4 2.1218 - 1.9280 0.96 2729 135 0.2876 0.3269 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.53 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 73.36 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.540 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.340 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) : -1.04550 REMARK 3 B22 (A**2) : 0.73090 REMARK 3 B33 (A**2) : 0.31460 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.17380 REMARK 3 B23 (A**2) : 0.00000 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 : 0.005 1252 REMARK 3 ANGLE : 0.877 1706 REMARK 3 CHIRALITY : 0.061 155 REMARK 3 PLANARITY : 0.003 224 REMARK 3 DIHEDRAL : 14.770 461 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 3SD4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000066057. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 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 MICROMAX-007 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 IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11693 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.928 REMARK 200 RESOLUTION RANGE LOW (A) : 30.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.200 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: MODEL GENERATED USING PHYRE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG 3000, 0.2 M AMMONIUM ACETATE, REMARK 280 0.1 M CACODYLIC ACID , PH 4.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.38050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 ARG A 9 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 69 O REMARK 470 ARG B 9 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 69 C O CB CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 135 O HOH A 169 2.02 REMARK 500 O HOH A 151 O HOH A 205 2.02 REMARK 500 O HOH B 180 O HOH B 193 2.02 REMARK 500 O HOH A 104 O HOH A 105 2.03 REMARK 500 O HOH B 175 O HOH B 183 2.05 REMARK 500 O HOH A 120 O HOH A 122 2.05 REMARK 500 O HOH A 183 O HOH A 201 2.06 REMARK 500 OD2 ASP A 61 O HOH A 167 2.09 REMARK 500 O HOH B 161 O HOH B 166 2.11 REMARK 500 O HOH A 171 O HOH A 174 2.11 REMARK 500 O HOH A 132 O HOH A 203 2.13 REMARK 500 O HOH A 165 O HOH B 151 2.15 REMARK 500 O HOH B 160 O HOH B 164 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HD1 HIS A 4 OE1 GLU B 14 2645 1.38 REMARK 500 O HOH A 101 O HOH B 114 1455 2.12 REMARK 500 ND1 HIS A 4 OE1 GLU B 14 2645 2.13 REMARK 500 O HOH A 177 O HOH B 168 1454 2.16 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 LYS A 26 31.17 75.89 REMARK 500 ARG A 49 -17.41 81.21 REMARK 500 LEU B 19 -179.29 -170.72 REMARK 500 LYS B 26 31.07 79.48 REMARK 500 ARG B 49 -24.56 88.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3P8D RELATED DB: PDB REMARK 900 ANOTHER TUDOR DOMAIN FROM THE SAME PROTEIN DBREF 3SD4 A 4 69 UNP Q9BVI0 PHF20_HUMAN 4 69 DBREF 3SD4 B 4 69 UNP Q9BVI0 PHF20_HUMAN 4 69 SEQADV 3SD4 GLY A -3 UNP Q9BVI0 EXPRESSION TAG SEQADV 3SD4 HIS A -2 UNP Q9BVI0 EXPRESSION TAG SEQADV 3SD4 MET A -1 UNP Q9BVI0 EXPRESSION TAG SEQADV 3SD4 GLY B -3 UNP Q9BVI0 EXPRESSION TAG SEQADV 3SD4 HIS B -2 UNP Q9BVI0 EXPRESSION TAG SEQADV 3SD4 MET B -1 UNP Q9BVI0 EXPRESSION TAG SEQRES 1 A 69 GLY HIS MET HIS PRO PRO ASN ARG ARG GLY ILE SER PHE SEQRES 2 A 69 GLU VAL GLY ALA GLN LEU GLU ALA ARG ASP ARG LEU LYS SEQRES 3 A 69 ASN TRP TYR PRO ALA HIS ILE GLU ASP ILE ASP TYR GLU SEQRES 4 A 69 GLU GLY LYS VAL LEU ILE HIS PHE LYS ARG TRP ASN HIS SEQRES 5 A 69 ARG TYR ASP GLU TRP PHE CYS TRP ASP SER PRO TYR LEU SEQRES 6 A 69 ARG PRO LEU GLU SEQRES 1 B 69 GLY HIS MET HIS PRO PRO ASN ARG ARG GLY ILE SER PHE SEQRES 2 B 69 GLU VAL GLY ALA GLN LEU GLU ALA ARG ASP ARG LEU LYS SEQRES 3 B 69 ASN TRP TYR PRO ALA HIS ILE GLU ASP ILE ASP TYR GLU SEQRES 4 B 69 GLU GLY LYS VAL LEU ILE HIS PHE LYS ARG TRP ASN HIS SEQRES 5 B 69 ARG TYR ASP GLU TRP PHE CYS TRP ASP SER PRO TYR LEU SEQRES 6 B 69 ARG PRO LEU GLU FORMUL 3 HOH *215(H2 O) HELIX 1 1 ASN A 51 ASP A 55 5 5 HELIX 2 2 ASN B 51 ASP B 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 GLU A 34 O LEU A 44 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 SHEET 1 B 5 GLU B 56 CYS B 59 0 SHEET 2 B 5 LYS B 42 PHE B 47 -1 N ILE B 45 O GLU B 56 SHEET 3 B 5 TRP B 28 ASP B 37 -1 N GLU B 34 O LEU B 44 SHEET 4 B 5 GLN B 18 ARG B 22 -1 N LEU B 19 O ALA B 31 SHEET 5 B 5 LEU B 65 ARG B 66 -1 O ARG B 66 N GLU B 20 CRYST1 37.746 60.761 37.750 90.00 112.82 90.00 P 1 21 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 0.026493 0.000000 0.011147 0.00000 SCALE2 0.000000 0.016458 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028740 0.00000