HEADER CHAPERONE 26-AUG-04 1XAO TITLE HSP40-YDJ1 DIMERIZATION DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL PROTEIN IMPORT PROTEIN MAS5; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: YDJ1 (RESIDUES 258-378); COMPND 5 SYNONYM: YDJ1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: MAS5, YDJ1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS BETA SHEETS, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR Y.WU,B.SHA REVDAT 4 14-FEB-24 1XAO 1 REMARK REVDAT 3 11-OCT-17 1XAO 1 REMARK REVDAT 2 24-FEB-09 1XAO 1 VERSN REVDAT 1 03-MAY-05 1XAO 0 JRNL AUTH Y.WU,J.LI,Z.JIN,Z.FU,B.SHA JRNL TITL THE CRYSTAL STRUCTURE OF THE C-TERMINAL FRAGMENT OF YEAST JRNL TITL 2 HSP40 YDJ1 REVEALS NOVEL DIMERIZATION MOTIF FOR HSP40 JRNL REF J.MOL.BIOL. V. 346 1005 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15701512 JRNL DOI 10.1016/J.JMB.2004.12.040 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1656796.840 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 15669 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) : 0.219 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1230 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 16.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 475 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 47 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.044 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1782 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 232 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.23000 REMARK 3 B22 (A**2) : 7.23000 REMARK 3 B33 (A**2) : -14.47000 REMARK 3 B12 (A**2) : 4.82000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.830 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 : 0.34 REMARK 3 BSOL : 63.75 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: NULL REMARK 4 REMARK 4 1XAO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000030145. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97936, 0.97947, 0.97242 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : ID REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15669 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 27.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 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) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.4 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CHLORIDE, PH 5.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 70.06367 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 140.12733 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 105.09550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 175.15917 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 35.03183 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: 6340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 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 ILE A 318 REMARK 465 PRO A 319 REMARK 465 LYS A 320 REMARK 465 TYR A 321 REMARK 465 GLY A 322 REMARK 465 GLY A 323 REMARK 465 ILE B 318 REMARK 465 PRO B 319 REMARK 465 LYS B 320 REMARK 465 TYR B 321 REMARK 465 GLY B 322 REMARK 465 GLY B 323 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 ALA A 360 75.20 -114.35 REMARK 500 LYS A 364 1.05 85.49 REMARK 500 PRO A 377 -34.52 -32.16 REMARK 500 ASP B 262 77.95 -112.67 REMARK 500 LYS B 364 -8.58 83.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NLT RELATED DB: PDB REMARK 900 TYPE I HSP40-YDJ1 PEPTIDE BINDING DOMAIN COMPLEXED WITH SUBSTRATE REMARK 900 RELATED ID: 1C3G RELATED DB: PDB REMARK 900 TYPE II HSP40-SIS1 PEPTIDE BINDING DOMAIN DBREF 1XAO A 258 378 UNP P25491 MAS5_YEAST 258 378 DBREF 1XAO B 258 378 UNP P25491 MAS5_YEAST 258 378 SEQRES 1 A 121 SER PHE LYS ARG ASP GLY ASP ASP LEU VAL TYR GLU ALA SEQRES 2 A 121 GLU ILE ASP LEU LEU THR ALA ILE ALA GLY GLY GLU PHE SEQRES 3 A 121 ALA LEU GLU HIS VAL SER GLY ASP TRP LEU LYS VAL GLY SEQRES 4 A 121 ILE VAL PRO GLY GLU VAL ILE ALA PRO GLY MET ARG LYS SEQRES 5 A 121 VAL ILE GLU GLY LYS GLY MET PRO ILE PRO LYS TYR GLY SEQRES 6 A 121 GLY TYR GLY ASN LEU ILE ILE LYS PHE THR ILE LYS PHE SEQRES 7 A 121 PRO GLU ASN HIS PHE THR SER GLU GLU ASN LEU LYS LYS SEQRES 8 A 121 LEU GLU GLU ILE LEU PRO PRO ARG ILE VAL PRO ALA ILE SEQRES 9 A 121 PRO LYS LYS ALA THR VAL ASP GLU CYS VAL LEU ALA ASP SEQRES 10 A 121 PHE ASP PRO ALA SEQRES 1 B 121 SER PHE LYS ARG ASP GLY ASP ASP LEU VAL TYR GLU ALA SEQRES 2 B 121 GLU ILE ASP LEU LEU THR ALA ILE ALA GLY GLY GLU PHE SEQRES 3 B 121 ALA LEU GLU HIS VAL SER GLY ASP TRP LEU LYS VAL GLY SEQRES 4 B 121 ILE VAL PRO GLY GLU VAL ILE ALA PRO GLY MET ARG LYS SEQRES 5 B 121 VAL ILE GLU GLY LYS GLY MET PRO ILE PRO LYS TYR GLY SEQRES 6 B 121 GLY TYR GLY ASN LEU ILE ILE LYS PHE THR ILE LYS PHE SEQRES 7 B 121 PRO GLU ASN HIS PHE THR SER GLU GLU ASN LEU LYS LYS SEQRES 8 B 121 LEU GLU GLU ILE LEU PRO PRO ARG ILE VAL PRO ALA ILE SEQRES 9 B 121 PRO LYS LYS ALA THR VAL ASP GLU CYS VAL LEU ALA ASP SEQRES 10 B 121 PHE ASP PRO ALA FORMUL 3 HOH *232(H2 O) HELIX 1 1 LEU A 274 GLY A 280 1 7 HELIX 2 2 SER A 342 LEU A 353 1 12 HELIX 3 3 LEU B 274 GLY B 280 1 7 HELIX 4 4 SER B 342 LEU B 353 1 12 SHEET 1 A 5 LYS A 260 ASP A 262 0 SHEET 2 A 5 ASP A 265 ASP A 273 -1 O ASP A 265 N ASP A 262 SHEET 3 A 5 LEU A 327 LYS A 334 1 O ILE A 328 N LEU A 266 SHEET 4 A 5 ARG A 308 ILE A 311 -1 N ILE A 311 O LEU A 327 SHEET 5 A 5 ALA B 373 ASP B 374 -1 O ALA B 373 N VAL A 310 SHEET 1 B 3 GLY A 281 GLU A 286 0 SHEET 2 B 3 TRP A 292 ILE A 297 -1 O ILE A 297 N GLY A 281 SHEET 3 B 3 VAL B 367 CYS B 370 1 O ASP B 368 N TRP A 292 SHEET 1 C 3 VAL A 367 VAL A 371 0 SHEET 2 C 3 TRP B 292 ILE B 297 1 O TRP B 292 N ASP A 368 SHEET 3 C 3 GLY B 281 GLU B 286 -1 N GLY B 281 O ILE B 297 SHEET 1 D 5 ALA A 373 ASP A 374 0 SHEET 2 D 5 ARG B 308 ILE B 311 -1 O VAL B 310 N ALA A 373 SHEET 3 D 5 LEU B 327 LYS B 334 -1 O ILE B 329 N LYS B 309 SHEET 4 D 5 ASP B 265 ASP B 273 1 N LEU B 266 O ILE B 328 SHEET 5 D 5 LYS B 260 ASP B 262 -1 N LYS B 260 O VAL B 267 CRYST1 49.631 49.631 210.191 90.00 90.00 120.00 P 61 12 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 0.020149 0.011633 0.000000 0.00000 SCALE2 0.000000 0.023266 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004758 0.00000