HEADER METAL BINDING PROTEIN/PEPTIDE 29-SEP-19 6L1F TITLE CRYSTAL STRUCTURE OF PHF20L1 TUDOR1 IN COMPLEX WITH K142ME1 DNMT1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THE K142ME1 DNMT1 PEPTIDE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: MLZ REPRESENT MONO-METHYLATED LYSINE; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PHD FINGER PROTEIN 20-LIKE PROTEIN 1; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: PLANT HOMEODOMAIN (PHD) FINGER PROTEIN 20-LIKE 1; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: PHF20L1, CGI-72; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHF20L1, TUDOR, APO, METAL BINDING PROTEIN-PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.Q.LV,J.GAO REVDAT 3 22-NOV-23 6L1F 1 REMARK REVDAT 2 30-SEP-20 6L1F 1 JRNL REVDAT 1 23-SEP-20 6L1F 0 JRNL AUTH M.LV,J.GAO,M.LI,R.MA,F.LI,Y.LIU,M.LIU,J.ZHANG,X.YAO,J.WU, JRNL AUTH 2 Y.SHI,Y.TANG,Y.PAN,Z.ZHANG,K.RUAN JRNL TITL CONFORMATIONAL SELECTION IN LIGAND RECOGNITION BY THE FIRST JRNL TITL 2 TUDOR DOMAIN OF PHF20L1. JRNL REF J PHYS CHEM LETT V. 11 7932 2020 JRNL REFN ESSN 1948-7185 JRNL PMID 32885980 JRNL DOI 10.1021/ACS.JPCLETT.0C02039 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 5921 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.340 REMARK 3 FREE R VALUE TEST SET COUNT : 553 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 33.2303 - 3.0152 0.99 1409 164 0.1810 0.2017 REMARK 3 2 3.0152 - 2.3935 1.00 1326 154 0.2143 0.2725 REMARK 3 3 2.3935 - 2.0910 1.00 1343 124 0.1956 0.2503 REMARK 3 4 2.0910 - 1.9000 0.97 1290 111 0.1960 0.2754 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.31 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 140 THROUGH 145) REMARK 3 ORIGIN FOR THE GROUP (A): -16.4359 23.5730 -1.6503 REMARK 3 T TENSOR REMARK 3 T11: 0.3737 T22: 0.2877 REMARK 3 T33: 0.3607 T12: 0.0067 REMARK 3 T13: 0.0228 T23: -0.0456 REMARK 3 L TENSOR REMARK 3 L11: 4.2223 L22: 1.7217 REMARK 3 L33: 2.3681 L12: -0.8179 REMARK 3 L13: -1.1304 L23: 1.9797 REMARK 3 S TENSOR REMARK 3 S11: -0.3157 S12: -0.4821 S13: 0.6096 REMARK 3 S21: 0.9015 S22: -0.0197 S23: 0.3470 REMARK 3 S31: -0.1589 S32: -0.0047 S33: -0.0479 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 3 THROUGH 69) REMARK 3 ORIGIN FOR THE GROUP (A): -9.5720 10.0745 -13.9429 REMARK 3 T TENSOR REMARK 3 T11: 0.1334 T22: 0.1473 REMARK 3 T33: 0.1374 T12: 0.0085 REMARK 3 T13: -0.0093 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 1.5895 L22: 2.2156 REMARK 3 L33: 1.2420 L12: 0.1794 REMARK 3 L13: 0.4965 L23: 0.3469 REMARK 3 S TENSOR REMARK 3 S11: 0.0140 S12: -0.0228 S13: -0.0231 REMARK 3 S21: -0.0088 S22: 0.0002 S23: 0.0083 REMARK 3 S31: 0.0281 S32: -0.0804 S33: 0.0034 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 6L1F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1300013985. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-18 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5921 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 33.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54100 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: 3SD4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG MME 2000, 0.1M SODIUM REMARK 280 CACODYLATE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 21.35100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.46600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.35100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.46600 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 APPLY THE FOLLOWING TO CHAINS: A, 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 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 B 1 REMARK 465 SER B 2 REMARK 465 ARG B 70 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 GLU B 39 CG CD OE1 OE2 DBREF 6L1F A 140 145 UNP P26358 DNMT1_HUMAN 140 145 DBREF 6L1F B 5 70 UNP A8MW92 P20L1_HUMAN 5 70 SEQADV 6L1F GLY B 1 UNP A8MW92 EXPRESSION TAG SEQADV 6L1F SER B 2 UNP A8MW92 EXPRESSION TAG SEQADV 6L1F HIS B 3 UNP A8MW92 EXPRESSION TAG SEQADV 6L1F MET B 4 UNP A8MW92 EXPRESSION TAG SEQRES 1 A 6 ARG SER MLZ SER ASP GLY SEQRES 1 B 70 GLY SER HIS MET PRO PRO ASN ARG PRO GLY ILE THR PHE SEQRES 2 B 70 GLU ILE GLY ALA ARG LEU GLU ALA LEU ASP TYR LEU GLN SEQRES 3 B 70 LYS TRP TYR PRO SER ARG ILE GLU LYS ILE ASP TYR GLU SEQRES 4 B 70 GLU GLY LYS MET LEU VAL HIS PHE GLU ARG TRP SER HIS SEQRES 5 B 70 ARG TYR ASP GLU TRP ILE TYR TRP ASP SER ASN ARG LEU SEQRES 6 B 70 ARG PRO LEU GLU ARG MODRES 6L1F MLZ A 142 LYS MODIFIED RESIDUE HET MLZ A 142 10 HETNAM MLZ N-METHYL-LYSINE FORMUL 1 MLZ C7 H16 N2 O2 FORMUL 3 HOH *32(H2 O) HELIX 1 AA1 SER B 51 ASP B 55 5 5 SHEET 1 AA1 5 GLU B 56 TYR B 59 0 SHEET 2 AA1 5 LYS B 42 PHE B 47 -1 N VAL B 45 O GLU B 56 SHEET 3 AA1 5 TRP B 28 ASP B 37 -1 N GLU B 34 O LEU B 44 SHEET 4 AA1 5 ARG B 18 LEU B 22 -1 N LEU B 19 O SER B 31 SHEET 5 AA1 5 LEU B 65 ARG B 66 -1 O ARG B 66 N GLU B 20 LINK C SER A 141 N MLZ A 142 1555 1555 1.33 LINK C MLZ A 142 N SER A 143 1555 1555 1.32 CRYST1 42.702 52.932 31.394 90.00 90.00 90.00 P 21 21 2 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 0.023418 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018892 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031853 0.00000