HEADER STRUCTURAL PROTEIN 05-MAR-23 8ILY TITLE CRYSTAL STRUCTURE OF THE RRM DOMAIN OF HUMAN SETD1A COMPND MOL_ID: 1; COMPND 2 MOLECULE: SET DOMAIN CONTAINING 1A, HISTONE LYSINE METHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 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: SETD1A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SETD1A, RRM, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.BAO,C.XU REVDAT 2 29-MAY-24 8ILY 1 REMARK REVDAT 1 26-APR-23 8ILY 0 JRNL AUTH S.BAO,C.XU JRNL TITL MOLECULAR INSIGHT INTO THE SETD1A/B N-TERMINAL REGION AND JRNL TITL 2 ITS INTERACTION WITH WDR82. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 658 136 2023 JRNL REFN ESSN 1090-2104 JRNL PMID 37030068 JRNL DOI 10.1016/J.BBRC.2023.03.064 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 18532 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.610 REMARK 3 FREE R VALUE TEST SET COUNT : 855 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 33.2000 - 3.0900 1.00 3035 152 0.1655 0.2076 REMARK 3 2 3.0900 - 2.4500 1.00 2977 113 0.1923 0.2420 REMARK 3 3 2.4500 - 2.1400 1.00 2926 155 0.1916 0.2679 REMARK 3 4 2.1400 - 1.9500 1.00 2951 146 0.1770 0.2206 REMARK 3 5 1.9500 - 1.8100 1.00 2941 147 0.1880 0.2743 REMARK 3 6 1.8100 - 1.7000 0.98 2847 142 0.2003 0.2545 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.177 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.374 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.71 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 : 0.007 1808 REMARK 3 ANGLE : 0.921 2436 REMARK 3 CHIRALITY : 0.065 279 REMARK 3 PLANARITY : 0.009 310 REMARK 3 DIHEDRAL : 5.344 244 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 8ILY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1300036011. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-22 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 : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18532 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 40.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05272 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.3200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4M SODIUM FORMATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K 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 15.83750 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 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 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 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 86 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 ARG A 106 -157.12 -113.79 REMARK 500 MET A 161 50.66 30.37 REMARK 500 ARG B 106 -157.48 -117.36 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8ILY A 89 195 UNP A0A804HLA6_HUMAN DBREF2 8ILY A A0A804HLA6 89 195 DBREF1 8ILY B 89 195 UNP A0A804HLA6_HUMAN DBREF2 8ILY B A0A804HLA6 89 195 SEQADV 8ILY GLY A 86 UNP A0A804HLA EXPRESSION TAG SEQADV 8ILY HIS A 87 UNP A0A804HLA EXPRESSION TAG SEQADV 8ILY MET A 88 UNP A0A804HLA EXPRESSION TAG SEQADV 8ILY GLY B 86 UNP A0A804HLA EXPRESSION TAG SEQADV 8ILY HIS B 87 UNP A0A804HLA EXPRESSION TAG SEQADV 8ILY MET B 88 UNP A0A804HLA EXPRESSION TAG SEQRES 1 A 110 GLY HIS MET GLY GLN ILE PRO LEU LYS GLU VAL THR PHE SEQRES 2 A 110 ALA ARG LEU ASN ASP ASN VAL ARG GLU THR PHE LEU LYS SEQRES 3 A 110 ASP MET CYS ARG LYS TYR GLY GLU VAL GLU GLU VAL GLU SEQRES 4 A 110 ILE LEU LEU HIS PRO ARG THR ARG LYS HIS LEU GLY LEU SEQRES 5 A 110 ALA ARG VAL LEU PHE THR SER THR ARG GLY ALA LYS GLU SEQRES 6 A 110 THR VAL LYS ASN LEU HIS LEU THR SER VAL MET GLY ASN SEQRES 7 A 110 ILE ILE HIS ALA GLN LEU ASP ILE LYS GLY GLN GLN ARG SEQRES 8 A 110 MET LYS TYR TYR GLU LEU ILE VAL ASN GLY SER TYR THR SEQRES 9 A 110 PRO GLN THR VAL PRO THR SEQRES 1 B 110 GLY HIS MET GLY GLN ILE PRO LEU LYS GLU VAL THR PHE SEQRES 2 B 110 ALA ARG LEU ASN ASP ASN VAL ARG GLU THR PHE LEU LYS SEQRES 3 B 110 ASP MET CYS ARG LYS TYR GLY GLU VAL GLU GLU VAL GLU SEQRES 4 B 110 ILE LEU LEU HIS PRO ARG THR ARG LYS HIS LEU GLY LEU SEQRES 5 B 110 ALA ARG VAL LEU PHE THR SER THR ARG GLY ALA LYS GLU SEQRES 6 B 110 THR VAL LYS ASN LEU HIS LEU THR SER VAL MET GLY ASN SEQRES 7 B 110 ILE ILE HIS ALA GLN LEU ASP ILE LYS GLY GLN GLN ARG SEQRES 8 B 110 MET LYS TYR TYR GLU LEU ILE VAL ASN GLY SER TYR THR SEQRES 9 B 110 PRO GLN THR VAL PRO THR FORMUL 3 HOH *247(H2 O) HELIX 1 AA1 ARG A 106 ARG A 115 1 10 HELIX 2 AA2 SER A 144 HIS A 156 1 13 HELIX 3 AA3 GLY A 173 ASN A 185 1 13 HELIX 4 AA4 ARG B 106 ARG B 115 1 10 HELIX 5 AA5 SER B 144 HIS B 156 1 13 HELIX 6 AA6 GLY B 173 GLY B 186 1 14 SHEET 1 AA1 4 VAL A 120 LEU A 127 0 SHEET 2 AA1 4 HIS A 134 PHE A 142 -1 O LEU A 141 N GLU A 121 SHEET 3 AA1 4 GLU A 95 ALA A 99 -1 N VAL A 96 O VAL A 140 SHEET 4 AA1 4 HIS A 166 LEU A 169 -1 O GLN A 168 N THR A 97 SHEET 1 AA2 2 SER A 159 VAL A 160 0 SHEET 2 AA2 2 ASN A 163 ILE A 164 -1 O ASN A 163 N VAL A 160 SHEET 1 AA3 4 VAL B 120 LEU B 127 0 SHEET 2 AA3 4 HIS B 134 PHE B 142 -1 O LEU B 141 N GLU B 121 SHEET 3 AA3 4 GLU B 95 ALA B 99 -1 N VAL B 96 O VAL B 140 SHEET 4 AA3 4 HIS B 166 LEU B 169 -1 O GLN B 168 N THR B 97 SHEET 1 AA4 2 SER B 159 VAL B 160 0 SHEET 2 AA4 2 ASN B 163 ILE B 164 -1 O ASN B 163 N VAL B 160 CRYST1 40.542 31.675 65.579 90.00 94.60 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 0.024666 0.000000 0.001985 0.00000 SCALE2 0.000000 0.031571 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015298 0.00000