HEADER LIGASE 21-MAR-20 6W92 TITLE HUMAN UHRF1 TTD DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE UHRF1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: INVERTED CCAAT BOX-BINDING PROTEIN OF 90 KDA,NUCLEAR PROTEIN COMPND 5 95,NUCLEAR ZINC FINGER PROTEIN NP95,HNP95,RING FINGER PROTEIN 106, COMPND 6 RING-TYPE E3 UBIQUITIN TRANSFERASE UHRF1,TRANSCRIPTION FACTOR ICBP90, COMPND 7 UBIQUITIN-LIKE PHD AND RING FINGER DOMAIN-CONTAINING PROTEIN 1, COMPND 8 HUHRF1,UBIQUITIN-LIKE-CONTAINING PHD AND RING FINGER DOMAINS PROTEIN COMPND 9 1; COMPND 10 EC: 2.3.2.27; COMPND 11 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: UHRF1, ICBP90, NP95, RNF106; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.C.CAMPBELL,L.CHANG,B.SANKARAN,D.W.YOUNG REVDAT 2 18-OCT-23 6W92 1 REMARK REVDAT 1 24-FEB-21 6W92 0 JRNL AUTH L.CHANG,J.CAMPBELL,I.O.RAJI,S.K.R.GUDURU,P.KANDEL,M.NGUYEN, JRNL AUTH 2 S.LIU,K.TRAN,N.K.VENUGOPAL,B.C.TAYLOR,M.V.HOLT,N.L.YOUNG, JRNL AUTH 3 E.L.G.SAMUEL,P.JAIN,C.SANTINI,B.SANKARAN,K.R.MACKENZIE, JRNL AUTH 4 D.W.YOUNG JRNL TITL DISCOVERY OF SMALL MOLECULES TARGETING THE TANDEM TUDOR JRNL TITL 2 DOMAIN OF THE EPIGENETIC FACTOR UHRF1 USING FRAGMENT-BASED JRNL TITL 3 LIGAND DISCOVERY. JRNL REF SCI REP V. 11 1121 2021 JRNL REFN ESSN 2045-2322 JRNL PMID 33441849 JRNL DOI 10.1038/S41598-020-80588-4 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 36990 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.410 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 42.3400 - 3.1300 1.00 2684 154 0.1753 0.1843 REMARK 3 2 3.1300 - 2.4900 1.00 2565 146 0.1735 0.1753 REMARK 3 3 2.4900 - 2.1700 1.00 2532 145 0.1632 0.1553 REMARK 3 4 2.1700 - 1.9700 1.00 2519 144 0.1542 0.1839 REMARK 3 5 1.9700 - 1.8300 1.00 2481 142 0.1649 0.1681 REMARK 3 6 1.8300 - 1.7200 1.00 2513 144 0.1720 0.1723 REMARK 3 7 1.7200 - 1.6400 1.00 2488 141 0.1721 0.2030 REMARK 3 8 1.6400 - 1.5700 1.00 2479 142 0.1733 0.2278 REMARK 3 9 1.5700 - 1.5100 1.00 2483 142 0.1755 0.1720 REMARK 3 10 1.5100 - 1.4500 1.00 2469 141 0.1851 0.2117 REMARK 3 11 1.4500 - 1.4100 1.00 2479 142 0.1826 0.2244 REMARK 3 12 1.4100 - 1.3700 1.00 2453 140 0.1955 0.1973 REMARK 3 13 1.3700 - 1.3300 0.99 2454 140 0.2066 0.2383 REMARK 3 14 1.3300 - 1.3000 0.97 2391 137 0.2304 0.2319 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) : 0.107 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.695 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.07 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 1296 REMARK 3 ANGLE : 0.898 1766 REMARK 3 CHIRALITY : 0.082 191 REMARK 3 PLANARITY : 0.007 236 REMARK 3 DIHEDRAL : 20.310 472 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 127 THROUGH 184 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.6435 -1.2316 -28.3700 REMARK 3 T TENSOR REMARK 3 T11: 0.0867 T22: 0.0898 REMARK 3 T33: 0.1137 T12: 0.0126 REMARK 3 T13: 0.0045 T23: 0.0185 REMARK 3 L TENSOR REMARK 3 L11: 0.6360 L22: 0.2658 REMARK 3 L33: 4.5428 L12: 0.3058 REMARK 3 L13: -0.4656 L23: -0.5514 REMARK 3 S TENSOR REMARK 3 S11: 0.0139 S12: 0.2115 S13: 0.1970 REMARK 3 S21: 0.0144 S22: 0.0596 S23: 0.0686 REMARK 3 S31: -0.3515 S32: -0.1438 S33: -0.0634 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 185 THROUGH 285 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.0599 -0.5671 -6.7768 REMARK 3 T TENSOR REMARK 3 T11: 0.0462 T22: 0.0446 REMARK 3 T33: 0.0648 T12: -0.0009 REMARK 3 T13: -0.0097 T23: 0.0137 REMARK 3 L TENSOR REMARK 3 L11: 1.4480 L22: 1.0359 REMARK 3 L33: 2.3167 L12: -0.8171 REMARK 3 L13: -1.4556 L23: 1.2067 REMARK 3 S TENSOR REMARK 3 S11: -0.0429 S12: -0.0122 S13: -0.0573 REMARK 3 S21: 0.0507 S22: -0.0127 S23: 0.0925 REMARK 3 S31: 0.0824 S32: -0.0515 S33: 0.0439 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 6W92 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247411. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37049 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 66.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4QQD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, PH = 5.5, 25 % W/V PEG REMARK 280 3350, PH 5.75, VAPOR DIFFUSION, HANGING 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 20.19000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.27500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.43500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.27500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.19000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.43500 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: 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: 9520 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 SER A 122 REMARK 465 ASN A 123 REMARK 465 ALA A 124 REMARK 465 ASP A 125 REMARK 465 GLU A 126 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 127 CG OD1 OD2 REMARK 470 MET A 128 CG SD CE REMARK 470 LEU A 136 CD1 CD2 REMARK 470 LYS A 138 CE NZ REMARK 470 MET A 150 CG SD CE REMARK 470 LYS A 164 CG CD CE NZ REMARK 470 ARG A 168 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 169 CG OD1 OD2 REMARK 470 SER A 174 OG REMARK 470 THR A 175 OG1 CG2 REMARK 470 ARG A 177 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 181 CG CD OE1 OE2 REMARK 470 GLU A 182 CG CD OE1 OE2 REMARK 470 LYS A 215 NZ REMARK 470 LYS A 235 CD CE NZ REMARK 470 ASP A 266 OD1 OD2 REMARK 470 LYS A 281 NZ REMARK 470 PRO A 285 CG CD 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 140 -13.53 87.69 REMARK 500 ARG A 211 -14.46 -150.45 REMARK 500 REMARK 500 REMARK: NULL DBREF 6W92 A 124 285 UNP Q96T88 UHRF1_HUMAN 135 296 SEQADV 6W92 SER A 122 UNP Q96T88 EXPRESSION TAG SEQADV 6W92 ASN A 123 UNP Q96T88 EXPRESSION TAG SEQRES 1 A 164 SER ASN ALA ASP GLU ASP MET TRP ASP GLU THR GLU LEU SEQRES 2 A 164 GLY LEU TYR LYS VAL ASN GLU TYR VAL ASP ALA ARG ASP SEQRES 3 A 164 THR ASN MET GLY ALA TRP PHE GLU ALA GLN VAL VAL ARG SEQRES 4 A 164 VAL THR ARG LYS ALA PRO SER ARG ASP GLU PRO CYS SER SEQRES 5 A 164 SER THR SER ARG PRO ALA LEU GLU GLU ASP VAL ILE TYR SEQRES 6 A 164 HIS VAL LYS TYR ASP ASP TYR PRO GLU ASN GLY VAL VAL SEQRES 7 A 164 GLN MET ASN SER ARG ASP VAL ARG ALA ARG ALA ARG THR SEQRES 8 A 164 ILE ILE LYS TRP GLN ASP LEU GLU VAL GLY GLN VAL VAL SEQRES 9 A 164 MET LEU ASN TYR ASN PRO ASP ASN PRO LYS GLU ARG GLY SEQRES 10 A 164 PHE TRP TYR ASP ALA GLU ILE SER ARG LYS ARG GLU THR SEQRES 11 A 164 ARG THR ALA ARG GLU LEU TYR ALA ASN VAL VAL LEU GLY SEQRES 12 A 164 ASP ASP SER LEU ASN ASP CYS ARG ILE ILE PHE VAL ASP SEQRES 13 A 164 GLU VAL PHE LYS ILE GLU ARG PRO FORMUL 2 HOH *224(H2 O) HELIX 1 AA1 LEU A 180 ASP A 183 5 4 HELIX 2 AA2 TYR A 193 ASN A 196 5 4 HELIX 3 AA3 LYS A 215 LEU A 219 5 5 SHEET 1 AA1 4 MET A 128 ASP A 130 0 SHEET 2 AA1 4 TRP A 153 LYS A 164 -1 O ARG A 163 N TRP A 129 SHEET 3 AA1 4 ILE A 185 TYR A 190 -1 O HIS A 187 N VAL A 159 SHEET 4 AA1 4 VAL A 198 ASN A 202 -1 O MET A 201 N TYR A 186 SHEET 1 AA2 4 MET A 128 ASP A 130 0 SHEET 2 AA2 4 TRP A 153 LYS A 164 -1 O ARG A 163 N TRP A 129 SHEET 3 AA2 4 TYR A 142 ARG A 146 -1 N VAL A 143 O ALA A 156 SHEET 4 AA2 4 VAL A 206 ARG A 207 -1 O ARG A 207 N ASP A 144 SHEET 1 AA3 4 VAL A 224 TYR A 229 0 SHEET 2 AA3 4 PHE A 239 GLU A 250 -1 O TYR A 241 N LEU A 227 SHEET 3 AA3 4 ARG A 255 VAL A 261 -1 O GLU A 256 N ARG A 249 SHEET 4 AA3 4 LEU A 268 ARG A 272 -1 O CYS A 271 N ALA A 259 CRYST1 40.380 54.870 66.550 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 0.024765 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018225 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015026 0.00000