HEADER CHAPERONE 06-APR-09 3GYW TITLE CRYSTAL STRUCTURE OF NUCLEOSOME ASSEMBLY PROTEIN FROM PLASMODIUM TITLE 2 FALCIPARUM AT 2.4 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSOME ASSEMBLY PROTEIN 1, PUTATIVE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 33-281 (UNP RESIDUES 45-293); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: 3D7; SOURCE 5 GENE: PFL0185C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS SIR, SIRAS, NUCLEOSOME ASSEMBLY PROTEIN, HISTONE RECOGNITION, KEYWDS 2 CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR M.YOGAVEL,J.GILL,A.SHARMA REVDAT 4 20-MAR-24 3GYW 1 REMARK REVDAT 3 13-JUL-11 3GYW 1 VERSN REVDAT 2 02-MAR-10 3GYW 1 JRNL REVDAT 1 12-MAY-09 3GYW 0 JRNL AUTH M.YOGAVEL,J.GILL,A.SHARMA JRNL TITL IODIDE-SAD, SIR AND SIRAS PHASING FOR STRUCTURE SOLUTION OF JRNL TITL 2 A NUCLEOSOME ASSEMBLY PROTEIN. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 65 618 2009 JRNL REFN ISSN 0907-4449 JRNL PMID 19465776 JRNL DOI 10.1107/S0907444909013171 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 8942 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 889 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1541 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 43 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) : 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3GYW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052479. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8943 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.20600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2M MAGNESIUM CHLORIDE, REMARK 280 PH 7.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 38.12000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.93500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.12000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.93500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 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 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 THR A 33 REMARK 465 ASP A 34 REMARK 465 ASN A 89 REMARK 465 GLY A 90 REMARK 465 GLU A 91 REMARK 465 ILE A 136 REMARK 465 LYS A 137 REMARK 465 LYS A 138 REMARK 465 ASN A 139 REMARK 465 LYS A 140 REMARK 465 GLU A 141 REMARK 465 LYS A 142 REMARK 465 LYS A 143 REMARK 465 GLU A 144 REMARK 465 LYS A 170 REMARK 465 CYS A 171 REMARK 465 VAL A 172 REMARK 465 ASP A 173 REMARK 465 CYS A 174 REMARK 465 ASP A 175 REMARK 465 ASN A 176 REMARK 465 GLU A 177 REMARK 465 PRO A 178 REMARK 465 VAL A 179 REMARK 465 LEU A 180 REMARK 465 LEU A 181 REMARK 465 LYS A 198 REMARK 465 LYS A 199 REMARK 465 ASN A 200 REMARK 465 VAL A 201 REMARK 465 VAL A 202 REMARK 465 LYS A 203 REMARK 465 LYS A 204 REMARK 465 GLN A 205 REMARK 465 HIS A 206 REMARK 465 ASN A 207 REMARK 465 LYS A 208 REMARK 465 ASN A 209 REMARK 465 SER A 210 REMARK 465 ARG A 211 REMARK 465 GLU A 212 REMARK 465 VAL A 213 REMARK 465 LYS A 214 REMARK 465 THR A 215 REMARK 465 VAL A 216 REMARK 465 GLN A 217 REMARK 465 GLN A 218 REMARK 465 THR A 219 REMARK 465 VAL A 220 REMARK 465 ASN A 221 REMARK 465 LYS A 233 REMARK 465 VAL A 234 REMARK 465 PRO A 235 REMARK 465 ASN A 236 REMARK 465 SER A 237 REMARK 465 ASN A 238 REMARK 465 VAL A 239 REMARK 465 ILE A 240 REMARK 465 LYS A 241 REMARK 465 GLN A 242 REMARK 465 LEU A 243 REMARK 465 SER A 244 REMARK 465 LYS A 245 REMARK 465 HIS A 246 REMARK 465 GLU A 247 REMARK 465 VAL A 248 REMARK 465 ALA A 249 REMARK 465 GLN A 250 REMARK 465 LEU A 251 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 O HOH A 288 O HOH A 291 2.16 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 LYS A 93 35.75 -87.98 REMARK 500 THR A 96 63.39 34.05 REMARK 500 LEU A 99 84.08 -152.99 REMARK 500 ASN A 195 97.01 -68.54 REMARK 500 ARG A 268 -56.45 -121.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FS3 RELATED DB: PDB REMARK 900 RELATED ID: 3GYV RELATED DB: PDB DBREF 3GYW A 33 281 UNP Q8I608 Q8I608_PLAF7 45 293 SEQRES 1 A 249 THR ASP LEU THR GLU GLU GLN LYS GLU THR LEU LYS LYS SEQRES 2 A 249 LEU LYS LEU TYR GLN LYS GLU TYR TYR ASP TYR GLU SER SEQRES 3 A 249 LYS PHE GLU TYR GLU LEU PHE LEU LEU ARG GLN LYS TYR SEQRES 4 A 249 HIS ASP LEU TYR GLY PRO ILE TYR ASP LYS ARG ARG GLU SEQRES 5 A 249 ALA LEU VAL GLY ASN GLY GLU ALA LYS ILE GLY THR PRO SEQRES 6 A 249 ASN LEU PRO GLU PHE TRP LEU ARG ALA LEU ARG ASN ASN SEQRES 7 A 249 ASN THR VAL SER HIS VAL ILE GLU ASP HIS ASP GLU GLU SEQRES 8 A 249 ILE LEU VAL TYR LEU ASN ASP ILE ARG CYS ASP TYR ILE SEQRES 9 A 249 LYS LYS ASN LYS GLU LYS LYS GLU GLY PHE ILE LEU SER SEQRES 10 A 249 PHE TYR PHE ALA THR ASN PRO PHE PHE SER ASN SER VAL SEQRES 11 A 249 LEU THR LYS THR TYR HIS MET LYS CYS VAL ASP CYS ASP SEQRES 12 A 249 ASN GLU PRO VAL LEU LEU HIS THR GLU ALA THR VAL ILE SEQRES 13 A 249 ASP TRP TYR ASP ASN LYS ASN ILE LEU LYS LYS ASN VAL SEQRES 14 A 249 VAL LYS LYS GLN HIS ASN LYS ASN SER ARG GLU VAL LYS SEQRES 15 A 249 THR VAL GLN GLN THR VAL ASN ARG ASP SER PHE PHE HIS SEQRES 16 A 249 PHE PHE THR SER HIS LYS VAL PRO ASN SER ASN VAL ILE SEQRES 17 A 249 LYS GLN LEU SER LYS HIS GLU VAL ALA GLN LEU GLU MET SEQRES 18 A 249 ILE ILE GLU GLY ASP TYR GLU VAL ALA LEU THR ILE LYS SEQRES 19 A 249 GLU ARG ILE ILE PRO TYR ALA VAL ASP TYR TYR LEU GLY SEQRES 20 A 249 ILE ILE FORMUL 2 HOH *43(H2 O) HELIX 1 1 THR A 36 GLY A 88 1 53 HELIX 2 2 GLU A 101 ASN A 109 1 9 HELIX 3 3 ASN A 110 HIS A 115 1 6 HELIX 4 4 GLU A 118 VAL A 126 1 9 HELIX 5 5 SER A 224 PHE A 229 5 6 HELIX 6 6 GLU A 252 ARG A 268 1 17 HELIX 7 7 ARG A 268 GLY A 279 1 12 SHEET 1 A 4 LEU A 128 ASP A 134 0 SHEET 2 A 4 PHE A 146 PHE A 152 -1 O TYR A 151 N ASP A 130 SHEET 3 A 4 VAL A 162 TYR A 167 -1 O LYS A 165 N LEU A 148 SHEET 4 A 4 THR A 183 ALA A 185 -1 O GLU A 184 N THR A 166 CRYST1 76.240 37.870 79.140 90.00 99.70 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 0.013117 0.000000 0.002244 0.00000 SCALE2 0.000000 0.026408 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012819 0.00000