PDB Short entry for 1YW5 HEADER ISOMERASE 17-FEB-05 1YW5 TITLE PEPTIDYL-PROLYL ISOMERASE ESS1 FROM CANDIDA ALBICANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL PROLYL CIS/TRANS ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.2.1.8; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDA ALBICANS; SOURCE 3 ORGANISM_TAXID: 5476; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(31); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS WW-DOMAIN, PPIASE DOMAIN, ORDERED LINKER, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.LI,H.LI,G.DEVASAHAYAM,T.GEMMILL,V.CHATURVEDI,S.D.HANES,P.VAN ROEY REVDAT 3 14-FEB-24 1YW5 1 REMARK REVDAT 2 24-FEB-09 1YW5 1 VERSN REVDAT 1 26-APR-05 1YW5 0 JRNL AUTH Z.LI,H.LI,G.DEVASAHAYAM,T.GEMMILL,V.CHATURVEDI,S.D.HANES, JRNL AUTH 2 P.VAN ROEY JRNL TITL THE STRUCTURE OF THE CANDIDA ALBICANS ESS1 PROLYL ISOMERASE JRNL TITL 2 REVEALS A WELL-ORDERED LINKER THAT RESTRICTS DOMAIN MOBILITY JRNL REF BIOCHEMISTRY V. 44 6180 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15835905 JRNL DOI 10.1021/BI050115L REMARK 2 REMARK 2 RESOLUTION. 1.60 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 504444.090 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 20204 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) : 0.200 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1991 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2730 REMARK 3 BIN R VALUE (WORKING SET) : 0.4210 REMARK 3 BIN FREE R VALUE : 0.4360 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 273 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1400 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 369 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.02000 REMARK 3 B22 (A**2) : -1.67000 REMARK 3 B33 (A**2) : 0.65000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.74000 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) : 0.14 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 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) : 1.250 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.830 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.970 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.860 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 40.12 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 1YW5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000031987. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20577 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.21100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR 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 (%): 38.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, MONOBASIC PHOSPHATE, AMMONIUM REMARK 280 ACETATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K 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 29.76000 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: 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 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 ASN A 11 -15.30 85.01 REMARK 500 ASN A 78 0.33 -68.67 REMARK 500 LYS A 82 67.99 37.57 REMARK 500 REMARK 500 REMARK: NULL DBREF 1YW5 A 1 177 UNP Q9C475 Q9C475_CANAL 1 177 SEQRES 1 A 177 MET ALA SER THR SER THR GLY LEU PRO PRO ASN TRP THR SEQRES 2 A 177 ILE ARG VAL SER ARG SER HIS ASN LYS GLU TYR PHE LEU SEQRES 3 A 177 ASN GLN SER THR ASN GLU SER SER TRP ASP PRO PRO TYR SEQRES 4 A 177 GLY THR ASP LYS GLU VAL LEU ASN ALA TYR ILE ALA LYS SEQRES 5 A 177 PHE LYS ASN ASN GLY TYR LYS PRO LEU VAL ASN GLU ASP SEQRES 6 A 177 GLY GLN VAL ARG VAL SER HIS LEU LEU ILE LYS ASN ASN SEQRES 7 A 177 GLN SER ARG LYS PRO LYS SER TRP LYS SER PRO ASP GLY SEQRES 8 A 177 ILE SER ARG THR ARG ASP GLU SER ILE GLN ILE LEU LYS SEQRES 9 A 177 LYS HIS LEU GLU ARG ILE LEU SER GLY GLU VAL LYS LEU SEQRES 10 A 177 SER GLU LEU ALA ASN THR GLU SER ASP CYS SER SER HIS SEQRES 11 A 177 ASP ARG GLY GLY ASP LEU GLY PHE PHE SER LYS GLY GLN SEQRES 12 A 177 MET GLN PRO PRO PHE GLU GLU ALA ALA PHE ASN LEU HIS SEQRES 13 A 177 VAL GLY GLU VAL SER ASN ILE ILE GLU THR ASN SER GLY SEQRES 14 A 177 VAL HIS ILE LEU GLN ARG THR GLY FORMUL 2 HOH *369(H2 O) HELIX 1 1 ASP A 42 ASN A 56 1 15 HELIX 2 2 THR A 95 SER A 112 1 18 HELIX 3 3 LYS A 116 SER A 125 1 10 HELIX 4 4 CYS A 127 GLY A 133 5 7 HELIX 5 5 GLN A 145 ASN A 154 1 10 SHEET 1 A 3 TRP A 12 VAL A 16 0 SHEET 2 A 3 GLU A 23 ASN A 27 -1 O TYR A 24 N ARG A 15 SHEET 3 A 3 SER A 33 SER A 34 -1 O SER A 34 N PHE A 25 SHEET 1 B 4 ASP A 135 PHE A 139 0 SHEET 2 B 4 VAL A 68 ILE A 75 -1 N VAL A 70 O LEU A 136 SHEET 3 B 4 GLY A 169 ARG A 175 -1 O VAL A 170 N ILE A 75 SHEET 4 B 4 ILE A 164 THR A 166 -1 N ILE A 164 O HIS A 171 CRYST1 29.840 59.520 44.860 90.00 91.04 90.00 P 1 21 1 2 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 0.033512 0.000000 0.000608 0.00000 SCALE2 0.000000 0.016801 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022295 0.00000