HEADER CHROMATIN REGULATOR 10-DEC-03 1UTU TITLE CRYSTAL STRUCTURE OF NOVEL PROTEIN EMSY TRUNCATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: EMSY; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-108; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CHROMATIN REGULATOR, CHROMATIN REGULATORS, ROYAL FAMILY DOMAIN EXPDTA X-RAY DIFFRACTION AUTHOR G.B.CHAVALI,B.P.BASU,A.J.DOHERTY REVDAT 3 05-JUL-17 1UTU 1 REMARK REVDAT 2 24-FEB-09 1UTU 1 VERSN REVDAT 1 13-OCT-05 1UTU 0 JRNL AUTH C.M.EKBLAD,G.B.CHAVALI,B.P.BASU,S.M.FREUND,D.VEPRINTSEV, JRNL AUTH 2 L.HUGHES-DAVIES,T.KOUZARIDES,A.J.DOHERTY,L.S.ITZHAKI JRNL TITL BINDING OF EMSY TO HP1BETA: IMPLICATIONS FOR RECRUITMENT OF JRNL TITL 2 HP1BETA AND BS69. JRNL REF EMBO REP. V. 6 675 2005 JRNL REFN ISSN 1469-221X JRNL PMID 15947784 JRNL DOI 10.1038/SJ.EMBOR.7400415 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN 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) : 27.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 876027.550 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 10796 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 524 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1601 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 87 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1503 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 132 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.81000 REMARK 3 B22 (A**2) : 3.71000 REMARK 3 B33 (A**2) : -0.91000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.34000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.21 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.31 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.850 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES 11,106 IN CHAIN A AND 10, 104 REMARK 3 IN CHAIN B WERE MODELED AS ALANINES. RESIDUES 1-10, 107- 108 IN REMARK 3 CHAIN A AND 1-9, 105-108 IN CHAIN B WERE NOT OBSERVED IN THE REMARK 3 STRUCTURE. REMARK 4 REMARK 4 1UTU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1290014178. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9491 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 27.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NACL, 20% PEG 3350, PH 6.9, PH REMARK 280 6.50 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 16.32100 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 EMSY PROTEIN IS AMPLIFIED IN BREAST CANCER AND INTERACTS WITH REMARK 400 BRCA2. THE EMSY N TERMINAL (ENT) DOMAIN IS FOUND IN OTHER REMARK 400 VERTEBRATE AND PLANT PROTEINS OF UNKNOWN FUNCTION, AND HAS A REMARK 400 COMPLETELY CONSERVED HISTIDINE RESIDUE THAT MAY BE FUNCTIONALLY REMARK 400 IMPORTANT. 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 1 REMARK 465 PRO A 2 REMARK 465 VAL A 3 REMARK 465 VAL A 4 REMARK 465 TRP A 5 REMARK 465 PRO A 6 REMARK 465 THR A 7 REMARK 465 LEU A 8 REMARK 465 LEU A 9 REMARK 465 ASP A 10 REMARK 465 PRO A 108 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 VAL B 3 REMARK 465 VAL B 4 REMARK 465 TRP B 5 REMARK 465 PRO B 6 REMARK 465 THR B 7 REMARK 465 LEU B 8 REMARK 465 LEU B 9 REMARK 465 LEU B 106 REMARK 465 VAL B 107 REMARK 465 PRO B 108 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 LEU A 106 CG CD1 CD2 REMARK 470 VAL A 107 CA C O CB CG1 CG2 REMARK 470 ASP B 10 CG OD1 OD2 REMARK 470 PRO B 104 CG CD REMARK 470 ARG B 105 CA C O CB CG CD NE REMARK 470 ARG B 105 CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 104 CA - N - CD ANGL. DEV. = -22.9 DEGREES REMARK 500 PRO B 101 CA - N - CD ANGL. DEV. = -15.5 DEGREES REMARK 500 PRO B 104 N - CA - CB ANGL. DEV. = 7.2 DEGREES 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 SER A 88 37.10 -140.67 REMARK 500 LEU A 102 -88.98 -64.69 REMARK 500 MET A 103 144.93 173.34 REMARK 500 ARG A 105 -3.00 93.23 REMARK 500 LEU A 106 -2.70 144.61 REMARK 500 SER B 84 15.79 -148.19 REMARK 500 MET B 103 -144.36 84.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LEU A 106 16.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UZ3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NOVEL PROTEIN EMSY DBREF 1UTU A 1 108 UNP Q8TE50 Q8TE50 1 108 DBREF 1UTU B 1 108 UNP Q8TE50 Q8TE50 1 108 SEQRES 1 A 108 MET PRO VAL VAL TRP PRO THR LEU LEU ASP LEU SER ARG SEQRES 2 A 108 ASP GLU CYS LYS ARG ILE LEU ARG LYS LEU GLU LEU GLU SEQRES 3 A 108 ALA TYR ALA GLY VAL ILE SER ALA LEU ARG ALA GLN GLY SEQRES 4 A 108 ASP LEU THR LYS GLU LYS LYS ASP LEU LEU GLY GLU LEU SEQRES 5 A 108 SER LYS VAL LEU SER ILE SER THR GLU ARG HIS ARG ALA SEQRES 6 A 108 GLU VAL ARG ARG ALA VAL ASN ASP GLU ARG LEU THR THR SEQRES 7 A 108 ILE ALA HIS ASN MET SER GLY PRO ASN SER SER SER GLU SEQRES 8 A 108 TRP SER ILE GLU GLY ARG ARG LEU VAL PRO LEU MET PRO SEQRES 9 A 108 ARG LEU VAL PRO SEQRES 1 B 108 MET PRO VAL VAL TRP PRO THR LEU LEU ASP LEU SER ARG SEQRES 2 B 108 ASP GLU CYS LYS ARG ILE LEU ARG LYS LEU GLU LEU GLU SEQRES 3 B 108 ALA TYR ALA GLY VAL ILE SER ALA LEU ARG ALA GLN GLY SEQRES 4 B 108 ASP LEU THR LYS GLU LYS LYS ASP LEU LEU GLY GLU LEU SEQRES 5 B 108 SER LYS VAL LEU SER ILE SER THR GLU ARG HIS ARG ALA SEQRES 6 B 108 GLU VAL ARG ARG ALA VAL ASN ASP GLU ARG LEU THR THR SEQRES 7 B 108 ILE ALA HIS ASN MET SER GLY PRO ASN SER SER SER GLU SEQRES 8 B 108 TRP SER ILE GLU GLY ARG ARG LEU VAL PRO LEU MET PRO SEQRES 9 B 108 ARG LEU VAL PRO FORMUL 3 HOH *132(H2 O) HELIX 1 1 SER A 12 GLY A 39 1 28 HELIX 2 2 THR A 42 LEU A 56 1 15 HELIX 3 3 SER A 59 ASP A 73 1 15 HELIX 4 4 ASP A 73 GLY A 85 1 13 HELIX 5 5 SER A 89 GLY A 96 1 8 HELIX 6 6 SER B 12 GLY B 39 1 28 HELIX 7 7 THR B 42 LEU B 56 1 15 HELIX 8 8 SER B 59 ASN B 72 1 14 HELIX 9 9 ASP B 73 GLY B 85 1 13 HELIX 10 10 SER B 89 GLY B 96 1 8 CRYST1 51.178 32.642 51.607 90.00 92.51 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 0.019540 0.000000 0.000856 0.00000 SCALE2 0.000000 0.030635 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019396 0.00000