PDB Short entry for 4NFA HEADER CELL CYCLE 31-OCT-13 4NFA TITLE STRUCTURE OF THE C-TERMINAL DOAMIN OF KNL1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN CASC5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KNL1 C-TERMINAL DOMAIN, UNP RESIDUES 2131-2337; COMPND 5 SYNONYM: ALL1-FUSED GENE FROM CHROMOSOME 15Q14 PROTEIN, AF15Q14, BUB- COMPND 6 LINKING KINETOCHORE PROTEIN, BLINKIN, CANCER SUSCEPTIBILITY CANDIDATE COMPND 7 GENE 5 PROTEIN, CANCER/TESTIS ANTIGEN 29, CT29, KINETOCHORE-NULL COMPND 8 PROTEIN 1, PROTEIN D40/AF15Q14; COMPND 9 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: CASC5, KIAA1570, KNL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RWD DOMAIN, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR A.PETROVIC,S.MOSALAGANTI,J.KELLER,M.MATTIUZZO,K.OVERLACK, AUTHOR 2 S.WOHLGEMUTH,S.PASQUALATO,S.RAUNSER,A.MUSACCHIO REVDAT 2 28-FEB-24 4NFA 1 REMARK REVDAT 1 19-MAR-14 4NFA 0 JRNL AUTH A.PETROVIC,S.MOSALAGANTI,J.KELLER,M.MATTIUZZO,K.OVERLACK, JRNL AUTH 2 V.KRENN,A.DE ANTONI,S.WOHLGEMUTH,V.CECATIELLO,S.PASQUALATO, JRNL AUTH 3 S.RAUNSER,A.MUSACCHIO JRNL TITL MODULAR ASSEMBLY OF RWD DOMAINS ON THE MIS12 COMPLEX JRNL TITL 2 UNDERLIES OUTER KINETOCHORE ORGANIZATION. JRNL REF MOL.CELL V. 53 591 2014 JRNL REFN ISSN 1097-2765 JRNL PMID 24530301 JRNL DOI 10.1016/J.MOLCEL.2014.01.019 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 10328 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 498 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 32.4159 - 3.9625 0.99 2545 131 0.1921 0.2232 REMARK 3 2 3.9625 - 3.1460 1.00 2447 116 0.1650 0.2289 REMARK 3 3 3.1460 - 2.7486 1.00 2433 121 0.1917 0.2682 REMARK 3 4 2.7486 - 2.4974 1.00 2405 130 0.2244 0.2890 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 79.29 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.740 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.06270 REMARK 3 B22 (A**2) : -2.06270 REMARK 3 B33 (A**2) : 4.12530 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1741 REMARK 3 ANGLE : 1.026 2364 REMARK 3 CHIRALITY : 0.062 263 REMARK 3 PLANARITY : 0.005 301 REMARK 3 DIHEDRAL : 17.870 624 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 4NFA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083129. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10352 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.497 REMARK 200 RESOLUTION RANGE LOW (A) : 32.413 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.350 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTO-RICKSHAW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 120-300 KSCN, 100 MM BISTRIS PROPANE REMARK 280 (PH 8.6-9.2), 17 % (V/V) PEG 3350 AND 1 MM DTT, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K, PH 9 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 29.58533 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 59.17067 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 59.17067 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 29.58533 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CL CL A2401 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2519 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2568 LIES ON A SPECIAL POSITION. 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 LYS A 2188 REMARK 465 THR A 2189 REMARK 465 CYS A 2190 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 SER A2105 OG REMARK 470 THR A2191 OG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 2184 O HOH A 2601 1.71 REMARK 500 REMARK 500 REMARK: NULL 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 A2126 -118.78 63.38 REMARK 500 ASN A2236 -119.63 59.05 REMARK 500 LEU A2292 79.54 -63.79 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 GOL A 2402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NF9 RELATED DB: PDB DBREF 4NFA A 2105 2311 UNP Q8NG31 CASC5_HUMAN 2117 2323 SEQRES 1 A 207 SER LEU SER GLU TRP ASP VAL VAL GLU TRP SER ASP ASP SEQRES 2 A 207 GLN ALA VAL PHE THR PHE VAL TYR ASP THR ILE GLN LEU SEQRES 3 A 207 THR ILE THR PHE GLU GLU SER VAL VAL GLY PHE PRO PHE SEQRES 4 A 207 LEU ASP LYS ARG TYR ARG LYS ILE VAL ASP VAL ASN PHE SEQRES 5 A 207 GLN SER LEU LEU ASP GLU ASP GLN ALA PRO PRO SER SER SEQRES 6 A 207 LEU LEU VAL HIS LYS LEU ILE PHE GLN TYR VAL GLU GLU SEQRES 7 A 207 LYS GLU SER TRP LYS LYS THR CYS THR THR GLN HIS GLN SEQRES 8 A 207 LEU PRO LYS MET LEU GLU GLU PHE SER LEU VAL VAL HIS SEQRES 9 A 207 HIS CYS ARG LEU LEU GLY GLU GLU ILE GLU TYR LEU LYS SEQRES 10 A 207 ARG TRP GLY PRO ASN TYR ASN LEU MET ASN ILE ASP ILE SEQRES 11 A 207 ASN ASN ASN GLU LEU ARG LEU LEU PHE SER SER SER ALA SEQRES 12 A 207 ALA PHE ALA LYS PHE GLU ILE THR LEU PHE LEU SER ALA SEQRES 13 A 207 TYR TYR PRO SER VAL PRO LEU PRO SER THR ILE GLN ASN SEQRES 14 A 207 HIS VAL GLY ASN THR SER GLN ASP ASP ILE ALA THR ILE SEQRES 15 A 207 LEU SER LYS VAL PRO LEU GLU ASN ASN TYR LEU LYS ASN SEQRES 16 A 207 VAL VAL LYS GLN ILE TYR GLN ASP LEU PHE GLN ASP HET CL A2401 1 HET GOL A2402 6 HET GOL A2403 6 HET GOL A2404 6 HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CL CL 1- FORMUL 3 GOL 3(C3 H8 O3) FORMUL 6 HOH *101(H2 O) HELIX 1 1 PRO A 2166 SER A 2185 1 20 HELIX 2 2 GLN A 2195 GLY A 2224 1 30 HELIX 3 3 PRO A 2225 TYR A 2227 5 3 HELIX 4 4 SER A 2279 VAL A 2290 1 12 HELIX 5 5 ASN A 2295 PHE A 2309 1 15 SHEET 1 A 4 VAL A2111 TRP A2114 0 SHEET 2 A 4 VAL A2120 TYR A2125 -1 O THR A2122 N GLU A2113 SHEET 3 A 4 ILE A2128 PHE A2134 -1 O ILE A2132 N PHE A2121 SHEET 4 A 4 ILE A2151 SER A2158 -1 O ASN A2155 N THR A2131 SHEET 1 B 4 LEU A2229 ASN A2235 0 SHEET 2 B 4 GLU A2238 SER A2245 -1 O ARG A2240 N ASP A2233 SHEET 3 B 4 ALA A2250 PHE A2257 -1 O LEU A2256 N LEU A2239 SHEET 4 B 4 SER A2269 VAL A2275 -1 O GLN A2272 N GLU A2253 CISPEP 1 TYR A 2262 PRO A 2263 0 4.32 SITE 1 AC1 2 TYR A2148 PRO A2268 SITE 1 AC2 7 LYS A2221 PRO A2225 LEU A2229 MET A2230 SITE 2 AC2 7 ASN A2231 ILE A2232 HOH A2590 SITE 1 AC3 6 VAL A2112 TRP A2114 LEU A2144 ASP A2145 SITE 2 AC3 6 LYS A2146 SER A2288 CRYST1 74.855 74.855 88.756 90.00 90.00 120.00 P 31 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 0.013359 0.007713 0.000000 0.00000 SCALE2 0.000000 0.015426 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011267 0.00000