HEADER DNA BINDING PROTEIN 26-SEP-19 6L0O TITLE WH DOMAIN OF HUMAN MCM8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA HELICASE MCM8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MINICHROMOSOME MAINTENANCE 8; COMPND 5 EC: 3.6.4.12; COMPND 6 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: MCM8, C20ORF154; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS WHD, WINGED HELIX, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,J.LI,L.LIU,H.ZENG REVDAT 3 27-MAR-24 6L0O 1 REMARK REVDAT 2 03-JUN-20 6L0O 1 JRNL REVDAT 1 29-APR-20 6L0O 0 JRNL AUTH H.ZENG,J.LI,H.XU,H.LI,Y.LIU JRNL TITL CRYSTAL STRUCTURE OF THE WINGED-HELIX DOMAIN OF MCM8. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 526 993 2020 JRNL REFN ESSN 1090-2104 JRNL PMID 32295713 JRNL DOI 10.1016/J.BBRC.2020.03.150 REMARK 2 REMARK 2 RESOLUTION. 1.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3139 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) : 1.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 23143 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.123 REMARK 3 R VALUE (WORKING SET) : 0.120 REMARK 3 FREE R VALUE : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.560 REMARK 3 FREE R VALUE TEST SET COUNT : 1981 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 33.6200 - 2.9200 1.00 1583 152 0.1436 0.1791 REMARK 3 2 2.9200 - 2.3100 1.00 1558 148 0.1211 0.1393 REMARK 3 3 2.3100 - 2.0200 0.99 1546 140 0.1063 0.1209 REMARK 3 4 2.0200 - 1.8400 0.99 1528 144 0.1110 0.1336 REMARK 3 5 1.8400 - 1.7100 0.98 1534 137 0.1033 0.1232 REMARK 3 6 1.7100 - 1.6000 0.98 1521 144 0.0999 0.1393 REMARK 3 7 1.6000 - 1.5200 0.98 1513 143 0.0972 0.1242 REMARK 3 8 1.5200 - 1.4600 0.97 1517 137 0.0946 0.1208 REMARK 3 9 1.4600 - 1.4000 0.97 1484 139 0.1056 0.1323 REMARK 3 10 1.4000 - 1.3500 0.96 1515 141 0.1139 0.1435 REMARK 3 11 1.3500 - 1.3100 0.96 1472 140 0.1160 0.1481 REMARK 3 12 1.3100 - 1.2700 0.96 1466 141 0.1151 0.1357 REMARK 3 13 1.2700 - 1.2400 0.96 1480 140 0.1202 0.1346 REMARK 3 14 1.2400 - 1.2100 0.93 1445 135 0.1338 0.1547 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) : 0.069 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.136 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.03 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 : 0.008 650 REMARK 3 ANGLE : 0.856 885 REMARK 3 CHIRALITY : 0.074 92 REMARK 3 PLANARITY : 0.006 118 REMARK 3 DIHEDRAL : 14.698 246 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 6L0O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1300013947. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-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 : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97930 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23189 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.210 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 20.30 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 51.5760 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.80 REMARK 200 R MERGE FOR SHELL (I) : 0.63300 REMARK 200 R SYM FOR SHELL (I) : 0.64400 REMARK 200 FOR SHELL : 5.714 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SIR2014 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0-2.2M (NH4)2SO4, 0.1M TRIS-HCL PH REMARK 280 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.82267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.64533 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.23400 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.05667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 8.41133 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: 170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 MET A 766 REMARK 465 ALA A 767 REMARK 465 ARG A 768 REMARK 465 SER A 769 REMARK 465 MET A 770 REMARK 465 SER A 771 REMARK 465 ASN A 772 REMARK 465 HIS A 844 REMARK 465 HIS A 845 REMARK 465 HIS A 846 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1081 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A1082 DISTANCE = 6.67 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 902 DBREF 6L0O A 770 840 UNP Q9UJA3 MCM8_HUMAN 770 840 SEQADV 6L0O MET A 766 UNP Q9UJA3 EXPRESSION TAG SEQADV 6L0O ALA A 767 UNP Q9UJA3 EXPRESSION TAG SEQADV 6L0O ARG A 768 UNP Q9UJA3 EXPRESSION TAG SEQADV 6L0O SER A 769 UNP Q9UJA3 EXPRESSION TAG SEQADV 6L0O HIS A 841 UNP Q9UJA3 EXPRESSION TAG SEQADV 6L0O HIS A 842 UNP Q9UJA3 EXPRESSION TAG SEQADV 6L0O HIS A 843 UNP Q9UJA3 EXPRESSION TAG SEQADV 6L0O HIS A 844 UNP Q9UJA3 EXPRESSION TAG SEQADV 6L0O HIS A 845 UNP Q9UJA3 EXPRESSION TAG SEQADV 6L0O HIS A 846 UNP Q9UJA3 EXPRESSION TAG SEQRES 1 A 81 MET ALA ARG SER MET SER ASN ARG SER THR ALA LYS ARG SEQRES 2 A 81 PHE ILE SER ALA LEU ASN ASN VAL ALA GLU ARG THR TYR SEQRES 3 A 81 ASN ASN ILE PHE GLN PHE HIS GLN LEU ARG GLN ILE ALA SEQRES 4 A 81 LYS GLU LEU ASN ILE GLN VAL ALA ASP PHE GLU ASN PHE SEQRES 5 A 81 ILE GLY SER LEU ASN ASP GLN GLY TYR LEU LEU LYS LYS SEQRES 6 A 81 GLY PRO LYS VAL TYR GLN LEU GLN THR MET HIS HIS HIS SEQRES 7 A 81 HIS HIS HIS HET SO4 A 901 5 HET SO4 A 902 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *82(H2 O) HELIX 1 AA1 ARG A 773 TYR A 791 1 19 HELIX 2 AA2 PHE A 797 LEU A 807 1 11 HELIX 3 AA3 ASP A 813 GLN A 824 1 12 SHEET 1 AA1 3 ILE A 794 GLN A 796 0 SHEET 2 AA1 3 VAL A 834 LEU A 837 -1 O TYR A 835 N PHE A 795 SHEET 3 AA1 3 LEU A 827 LYS A 829 -1 N LEU A 828 O GLN A 836 SITE 1 AC1 4 ARG A 778 ASN A 822 LYS A 829 HOH A1045 SITE 1 AC2 4 LYS A 777 PHE A 797 HIS A 798 ARG A 801 CRYST1 52.062 52.062 50.468 90.00 90.00 120.00 P 61 6 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 0.019208 0.011090 0.000000 0.00000 SCALE2 0.000000 0.022179 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019815 0.00000