HEADER DNA BINDING PROTEIN 28-OCT-13 4NE3 TITLE HUMAN MHF1-MHF2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CENTROMERE PROTEIN S; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CENP-S, APOPTOSIS-INDUCING TAF9-LIKE DOMAIN-CONTAINING COMPND 5 PROTEIN 1, FANCM-INTERACTING HISTONE FOLD PROTEIN 1, FANCONI ANEMIA- COMPND 6 ASSOCIATED POLYPEPTIDE OF 16 KDA; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: CENTROMERE PROTEIN X; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: CENP-X, FANCM-INTERACTING HISTONE FOLD PROTEIN 2, FANCONI COMPND 12 ANEMIA-ASSOCIATED POLYPEPTIDE OF 10 KDA, RETINOIC ACID-INDUCIBLE GENE COMPND 13 D9 PROTEIN HOMOLOG, STIMULATED BY RETINOIC ACID GENE 13 PROTEIN COMPND 14 HOMOLOG; COMPND 15 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: APITD1, CENPS, FAAP16, MHF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 ROSSETTA; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: STRA13, CENPX, FAAP10, MHF2; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21 ROSSETTA KEYWDS HISTONE FOLD, DNA REPAIR, GENOME MAINTENANCE, FANCONI ANEMIA, FANCM, KEYWDS 2 DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Q.ZHAO,D.SARO,A.SACHPATZIDIS,P.SUNG,Y.XIONG REVDAT 2 12-FEB-14 4NE3 1 JRNL REVDAT 1 25-DEC-13 4NE3 0 JRNL AUTH Q.ZHAO,D.SARO,A.SACHPATZIDIS,T.R.SINGH,D.SCHLINGMAN, JRNL AUTH 2 X.F.ZHENG,A.MACK,M.S.TSAI,S.MOCHRIE,L.REGAN,A.R.MEETEI, JRNL AUTH 3 P.SUNG,Y.XIONG JRNL TITL THE MHF COMPLEX SENSES BRANCHED DNA BY BINDING A PAIR OF JRNL TITL 2 CROSSOVER DNA DUPLEXES. JRNL REF NAT COMMUN V. 5 2987 2014 JRNL REFN ESSN 2041-1723 JRNL PMID 24390579 JRNL DOI 10.1038/NCOMMS3987 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 16358 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 826 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 28.1054 - 3.2707 0.97 2597 130 0.2282 0.2228 REMARK 3 2 3.2707 - 2.5967 0.99 2592 131 0.2185 0.2722 REMARK 3 3 2.5967 - 2.2686 1.00 2588 140 0.2137 0.2395 REMARK 3 4 2.2686 - 2.0612 1.00 2597 129 0.2322 0.2631 REMARK 3 5 2.0612 - 1.9135 1.00 2579 163 0.2688 0.3355 REMARK 3 6 1.9135 - 1.8007 0.99 2579 133 0.3264 0.3773 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.06 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 61.38 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.90430 REMARK 3 B22 (A**2) : -0.98020 REMARK 3 B33 (A**2) : -6.92420 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : 2.13730 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 1341 REMARK 3 ANGLE : 0.928 1801 REMARK 3 CHIRALITY : 0.063 214 REMARK 3 PLANARITY : 0.003 229 REMARK 3 DIHEDRAL : 13.085 507 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 4NE3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-13. REMARK 100 THE RCSB ID CODE IS RCSB083086. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16358 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.801 REMARK 200 RESOLUTION RANGE LOW (A) : 28.102 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 (%): 47.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 30.98450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.47250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.98450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.47250 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -107.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 HOH A 228 LIES ON A SPECIAL POSITION. 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 ARG A 88 CG CD NE CZ NH1 NH2 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 88 -72.40 -16.17 REMARK 500 ALA A 104 31.55 -83.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NE1 RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 4NDY RELATED DB: PDB REMARK 900 PROTEIN-DNA COMPLEX REMARK 900 RELATED ID: 4NE5 RELATED DB: PDB REMARK 900 SAME COMPLEX REMARK 900 RELATED ID: 4NE6 RELATED DB: PDB REMARK 900 SAME COMPLEX DBREF 4NE3 A 14 105 UNP Q8N2Z9 CENPS_HUMAN 14 105 DBREF 4NE3 B 8 81 UNP A8MT69 CENPX_HUMAN 8 81 SEQADV 4NE3 ALA A 39 UNP Q8N2Z9 GLU 39 CONFLICT SEQADV 4NE3 ALA A 106 UNP Q8N2Z9 EXPRESSION TAG SEQRES 1 A 93 SER TYR GLN GLN ARG LEU LYS ALA ALA VAL HIS TYR THR SEQRES 2 A 93 VAL GLY CYS LEU CYS GLU GLU VAL ALA LEU ASP LYS ALA SEQRES 3 A 93 MSE GLN PHE SER LYS GLN THR ILE ALA ALA ILE SER GLU SEQRES 4 A 93 LEU THR PHE ARG GLN CYS GLU ASN PHE ALA LYS ASP LEU SEQRES 5 A 93 GLU MSE PHE ALA ARG HIS ALA LYS ARG THR THR ILE ASN SEQRES 6 A 93 THR GLU ASP VAL LYS LEU LEU ALA ARG ARG SER ASN SER SEQRES 7 A 93 LEU LEU LYS TYR ILE THR ASP LYS SER GLU GLU ILE ALA SEQRES 8 A 93 GLN ALA SEQRES 1 B 74 SER GLY PHE ARG LYS GLU LEU VAL SER ARG LEU LEU HIS SEQRES 2 B 74 LEU HIS PHE LYS ASP ASP LYS THR LYS VAL SER GLY ASP SEQRES 3 B 74 ALA LEU GLN LEU MSE VAL GLU LEU LEU LYS VAL PHE VAL SEQRES 4 B 74 VAL GLU ALA ALA VAL ARG GLY VAL ARG GLN ALA GLN ALA SEQRES 5 B 74 GLU ASP ALA LEU ARG VAL ASP VAL ASP GLN LEU GLU LYS SEQRES 6 B 74 VAL LEU PRO GLN LEU LEU LEU ASP PHE MODRES 4NE3 MSE A 40 MET SELENOMETHIONINE MODRES 4NE3 MSE A 67 MET SELENOMETHIONINE MODRES 4NE3 MSE B 38 MET SELENOMETHIONINE HET MSE A 40 8 HET MSE A 67 8 HET MSE B 38 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 3 HOH *56(H2 O) HELIX 1 1 SER A 14 ALA A 39 1 26 HELIX 2 2 SER A 43 ALA A 72 1 30 HELIX 3 3 ASN A 78 ALA A 86 1 9 HELIX 4 4 SER A 89 ALA A 104 1 16 HELIX 5 5 ARG B 11 LEU B 21 1 11 HELIX 6 6 SER B 31 GLU B 60 1 30 HELIX 7 7 ASP B 66 PHE B 81 1 16 SHEET 1 A 2 THR A 76 ILE A 77 0 SHEET 2 A 2 LYS B 29 VAL B 30 1 O LYS B 29 N ILE A 77 LINK C ALA A 39 N MSE A 40 1555 1555 1.33 LINK C MSE A 40 N GLN A 41 1555 1555 1.32 LINK C GLU A 66 N MSE A 67 1555 1555 1.33 LINK C MSE A 67 N PHE A 68 1555 1555 1.33 LINK C LEU B 37 N MSE B 38 1555 1555 1.33 LINK C MSE B 38 N VAL B 39 1555 1555 1.33 CRYST1 61.969 52.945 60.283 90.00 114.91 90.00 C 1 2 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 0.016137 0.000000 0.007494 0.00000 SCALE2 0.000000 0.018888 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018290 0.00000