HEADER ISOMERASE 26-JUN-02 1H0P TITLE CYCLOPHILIN_5 FROM C. ELEGANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 23-204; COMPND 5 SYNONYM: PPIASE, ROTAMASE, CYCLOPHILIN-5; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS ISOMERASE, ROTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR N.C.PICKEN,S.ESCHENLAUER,P.TAYLOR,A.P.PAGE,M.D.WALKINSHAW REVDAT 4 13-DEC-23 1H0P 1 REMARK REVDAT 3 22-MAY-19 1H0P 1 REMARK REVDAT 2 24-FEB-09 1H0P 1 VERSN REVDAT 1 12-SEP-02 1H0P 0 JRNL AUTH N.C.PICKEN,S.ESCHENLAUER,P.TAYLOR,A.P.PAGE,M.D.WALKINSHAW JRNL TITL STRUCTURAL AND BIOLOGICAL CHARACTERISATION OF THE JRNL TITL 2 GUT-ASSOCIATED CYCLOPHILIN B ISOFORMS FROM CAENORHABDITIS JRNL TITL 3 ELEGANS JRNL REF J.MOL.BIOL. V. 322 15 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12215411 JRNL DOI 10.1016/S0022-2836(02)00712-X REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.180 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.182 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1087 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 21525 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.169 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.172 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 919 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 17035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1402 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1608.3 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6488 REMARK 3 NUMBER OF RESTRAINTS : 5794 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.035 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.049 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.016 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.069 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1H0P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1290011040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21525 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 24.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 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: PDB ENTRY 1E8K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0, PEG 4000, LITHIUM CHLORIDE, PH REMARK 280 6.00 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 13.74633 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 27.49267 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 20.61950 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 34.36583 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 6.87317 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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: 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 ARG A 29 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 TYR A 31 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 164 NE - CZ - NH2 ANGL. DEV. = -3.4 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 PHE A 84 -76.77 -149.76 REMARK 500 ASP A 192 -74.05 -23.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTT A1204 DBREF 1H0P A 22 203 UNP P52013 CYP5_CAEEL 23 204 SEQADV 1H0P ARG A 29 UNP P52013 LYS 30 ENGINEERED MUTATION SEQRES 1 A 182 LYS GLY PRO LYS VAL THR ASP ARG VAL TYR PHE ASP MET SEQRES 2 A 182 GLU ILE GLY GLY LYS PRO ILE GLY ARG ILE VAL ILE GLY SEQRES 3 A 182 LEU PHE GLY LYS THR VAL PRO LYS THR ALA THR ASN PHE SEQRES 4 A 182 ILE GLU LEU ALA LYS LYS PRO LYS GLY GLU GLY TYR PRO SEQRES 5 A 182 GLY SER LYS PHE HIS ARG VAL ILE ALA ASP PHE MET ILE SEQRES 6 A 182 GLN GLY GLY ASP PHE THR ARG GLY ASP GLY THR GLY GLY SEQRES 7 A 182 ARG SER ILE TYR GLY GLU LYS PHE ALA ASP GLU ASN PHE SEQRES 8 A 182 LYS LEU LYS HIS TYR GLY ALA GLY TRP LEU SER MET ALA SEQRES 9 A 182 ASN ALA GLY ALA ASP THR ASN GLY SER GLN PHE PHE ILE SEQRES 10 A 182 THR THR VAL LYS THR PRO TRP LEU ASP GLY ARG HIS VAL SEQRES 11 A 182 VAL PHE GLY LYS ILE LEU GLU GLY MET ASP VAL VAL ARG SEQRES 12 A 182 LYS ILE GLU GLN THR GLU LYS LEU PRO GLY ASP ARG PRO SEQRES 13 A 182 LYS GLN ASP VAL ILE ILE ALA ALA SER GLY HIS ILE ALA SEQRES 14 A 182 VAL ASP THR PRO PHE SER VAL GLU ARG GLU ALA VAL VAL HET DTT A1204 8 HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETSYN DTT 1,4-DITHIOTHREITOL FORMUL 2 DTT C4 H10 O2 S2 FORMUL 3 HOH *201(H2 O) HELIX 1 1 VAL A 53 LYS A 66 1 14 HELIX 2 2 THR A 143 ASP A 147 5 5 HELIX 3 3 GLY A 159 GLN A 168 1 10 SHEET 1 AA 8 ARG A 79 ILE A 81 0 SHEET 2 AA 8 MET A 85 GLY A 88 -1 O MET A 85 N ILE A 81 SHEET 3 AA 8 PHE A 136 THR A 139 -1 O PHE A 136 N GLY A 88 SHEET 4 AA 8 TRP A 121 MET A 124 -1 O TRP A 121 N THR A 139 SHEET 5 AA 8 VAL A 152 GLU A 158 -1 N PHE A 153 O LEU A 122 SHEET 6 AA 8 LYS A 39 LEU A 48 -1 O VAL A 45 N LEU A 157 SHEET 7 AA 8 LYS A 25 ILE A 36 -1 N THR A 27 O LEU A 48 SHEET 8 AA 8 VAL A 181 SER A 196 -1 O ILE A 182 N GLU A 35 SHEET 1 AB 2 LYS A 171 LEU A 172 0 SHEET 2 AB 2 ARG A 176 PRO A 177 -1 O ARG A 176 N LEU A 172 SITE 1 AC1 6 ARG A 79 ASN A 126 LEU A 146 ARG A 149 SITE 2 AC1 6 HIS A 150 HOH A2138 CRYST1 94.115 94.115 41.239 90.00 90.00 120.00 P 61 6 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 0.010625 0.006134 0.000000 0.00000 SCALE2 0.000000 0.012269 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024249 0.00000