HEADER CELL CYCLE 02-SEP-16 5LSI TITLE CRYSTAL STRUCTURE OF THE KINETOCHORE MIS12 COMPLEX HEAD2 SUBDOMAIN TITLE 2 CONTAINING DSN1 AND NSL1 FRAGMENTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: KINETOCHORE-ASSOCIATED PROTEIN DSN1 HOMOLOG; COMPND 3 CHAIN: D; COMPND 4 FRAGMENT: HEAD2 DOMAIN, UNP RESIDUES 68-200; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: KINETOCHORE-ASSOCIATED PROTEIN NSL1 HOMOLOG; COMPND 8 CHAIN: E; COMPND 9 FRAGMENT: UNP RESIDUES 29-99; COMPND 10 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: DSN1, C20ORF172, MIS13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: CODON-PLUS-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-2RBS; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: NSL1, C1ORF48, DC31, DC8, MIS14; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_VARIANT: CODON-PLUS-RIL; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGEX-2RBS KEYWDS ALPHA-HELICAL, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR I.R.VETTER,A.PETROVIC,J.KELLER,Y.LIU REVDAT 3 17-JAN-24 5LSI 1 REMARK REVDAT 2 07-DEC-16 5LSI 1 JRNL REVDAT 1 16-NOV-16 5LSI 0 JRNL AUTH A.PETROVIC,J.KELLER,Y.LIU,K.OVERLACK,J.JOHN,Y.N.DIMITROVA, JRNL AUTH 2 S.JENNI,S.VAN GERWEN,P.STEGE,S.WOHLGEMUTH,P.ROMBAUT, JRNL AUTH 3 F.HERZOG,S.C.HARRISON,I.R.VETTER,A.MUSACCHIO JRNL TITL STRUCTURE OF THE MIS12 COMPLEX AND MOLECULAR BASIS OF ITS JRNL TITL 2 INTERACTION WITH CENP-C AT HUMAN KINETOCHORES. JRNL REF CELL V. 167 1028 2016 JRNL REFN ISSN 1097-4172 JRNL PMID 27881301 JRNL DOI 10.1016/J.CELL.2016.10.005 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 11837 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 593 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 43.7646 - 3.1778 1.00 2922 154 0.1891 0.2215 REMARK 3 2 3.1778 - 2.5224 1.00 2811 148 0.2244 0.2387 REMARK 3 3 2.5224 - 2.2036 1.00 2755 146 0.2398 0.2891 REMARK 3 4 2.2036 - 2.0021 1.00 2756 145 0.2901 0.3147 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.50 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 : 0.003 1252 REMARK 3 ANGLE : 0.516 1682 REMARK 3 CHIRALITY : 0.037 185 REMARK 3 PLANARITY : 0.003 221 REMARK 3 DIHEDRAL : 16.916 764 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 5LSI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1200001285. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11845 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 43.754 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.10 REMARK 200 R MERGE (I) : 0.24200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 18.10 REMARK 200 R MERGE FOR SHELL (I) : 1.35500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.120 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: 5LSK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 0.2M POTASSIUM REMARK 280 SODIUM PHOSPHATE, 0.1M SODIUM CITRATE PH 5.6, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 54.89333 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 27.44667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.44667 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 54.89333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E 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 D 67 REMARK 465 SER D 68 REMARK 465 HIS D 69 REMARK 465 GLN D 70 REMARK 465 GLU D 71 REMARK 465 ARG D 72 REMARK 465 LEU D 73 REMARK 465 GLN D 74 REMARK 465 SER D 75 REMARK 465 LYS D 76 REMARK 465 SER D 77 REMARK 465 LEU D 78 REMARK 465 HIS D 79 REMARK 465 LEU D 80 REMARK 465 SER D 81 REMARK 465 PRO D 82 REMARK 465 GLN D 83 REMARK 465 GLU D 84 REMARK 465 GLN D 85 REMARK 465 SER D 86 REMARK 465 ALA D 87 REMARK 465 SER D 88 REMARK 465 TYR D 89 REMARK 465 GLN D 90 REMARK 465 ASP D 91 REMARK 465 ARG D 92 REMARK 465 ARG D 93 REMARK 465 GLN D 94 REMARK 465 SER D 95 REMARK 465 TRP D 96 REMARK 465 ARG D 97 REMARK 465 ARG D 98 REMARK 465 ALA D 99 REMARK 465 SER D 100 REMARK 465 MET D 101 REMARK 465 LYS D 102 REMARK 465 GLU D 103 REMARK 465 THR D 104 REMARK 465 ASN D 105 REMARK 465 ARG D 106 REMARK 465 ARG D 107 REMARK 465 LYS D 108 REMARK 465 SER D 109 REMARK 465 LEU D 110 REMARK 465 HIS D 111 REMARK 465 PRO D 112 REMARK 465 ILE D 113 REMARK 465 HIS D 114 REMARK 465 GLN D 115 REMARK 465 LYS D 198 REMARK 465 ALA D 199 REMARK 465 SER D 200 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 ASP D 155 46.33 -77.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 E 101 DBREF 5LSI D 68 200 UNP Q9H410 DSN1_HUMAN 68 200 DBREF 5LSI E 29 99 UNP Q96IY1 NSL1_HUMAN 29 99 SEQADV 5LSI MET D 67 UNP Q9H410 INITIATING METHIONINE SEQADV 5LSI GLY E 24 UNP Q96IY1 EXPRESSION TAG SEQADV 5LSI PRO E 25 UNP Q96IY1 EXPRESSION TAG SEQADV 5LSI LEU E 26 UNP Q96IY1 EXPRESSION TAG SEQADV 5LSI GLY E 27 UNP Q96IY1 EXPRESSION TAG SEQADV 5LSI SER E 28 UNP Q96IY1 EXPRESSION TAG SEQRES 1 D 134 MET SER HIS GLN GLU ARG LEU GLN SER LYS SER LEU HIS SEQRES 2 D 134 LEU SER PRO GLN GLU GLN SER ALA SER TYR GLN ASP ARG SEQRES 3 D 134 ARG GLN SER TRP ARG ARG ALA SER MET LYS GLU THR ASN SEQRES 4 D 134 ARG ARG LYS SER LEU HIS PRO ILE HIS GLN GLY ILE THR SEQRES 5 D 134 GLU LEU SER ARG SER ILE SER VAL ASP LEU ALA GLU SER SEQRES 6 D 134 LYS ARG LEU GLY CYS LEU LEU LEU SER SER PHE GLN PHE SEQRES 7 D 134 SER ILE GLN LYS LEU GLU PRO PHE LEU ARG ASP THR LYS SEQRES 8 D 134 GLY PHE SER LEU GLU SER PHE ARG ALA LYS ALA SER SER SEQRES 9 D 134 LEU SER GLU GLU LEU LYS HIS PHE ALA ASP GLY LEU GLU SEQRES 10 D 134 THR ASP GLY THR LEU GLN LYS CYS PHE GLU ASP SER ASN SEQRES 11 D 134 GLY LYS ALA SER SEQRES 1 E 76 GLY PRO LEU GLY SER SER ALA THR PRO ARG GLU ASP PHE SEQRES 2 E 76 ARG VAL ARG CYS THR SER LYS ARG ALA VAL THR GLU MET SEQRES 3 E 76 LEU GLN LEU CYS GLY ARG PHE VAL GLN LYS LEU GLY ASP SEQRES 4 E 76 ALA LEU PRO GLU GLU ILE ARG GLU PRO ALA LEU ARG ASP SEQRES 5 E 76 ALA GLN TRP THR PHE GLU SER ALA VAL GLN GLU ASN ILE SEQRES 6 E 76 SER ILE ASN GLY GLN ALA TRP GLN GLU ALA SER HET SO4 E 101 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *53(H2 O) HELIX 1 AA1 THR D 118 SER D 123 1 6 HELIX 2 AA2 ALA D 129 GLU D 150 1 22 HELIX 3 AA3 PRO D 151 LEU D 153 5 3 HELIX 4 AA4 SER D 160 ASP D 185 1 26 HELIX 5 AA5 LEU D 188 GLU D 193 5 6 HELIX 6 AA6 SER E 42 LYS E 59 1 18 HELIX 7 AA7 LEU E 60 LEU E 64 5 5 HELIX 8 AA8 ILE E 68 GLU E 86 1 19 SHEET 1 AA1 2 VAL E 38 CYS E 40 0 SHEET 2 AA1 2 ILE E 88 ILE E 90 1 O SER E 89 N CYS E 40 SITE 1 AC1 4 GLN D 143 LYS D 190 GLY E 24 SER E 29 CRYST1 59.640 59.640 82.340 90.00 90.00 120.00 P 32 2 1 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 0.016767 0.009681 0.000000 0.00000 SCALE2 0.000000 0.019361 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012145 0.00000