HEADER ISOMERASE(PEPTIDYL-PROLYL CIS-TRANS) 10-FEB-00 1DYW TITLE BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF A DIVERGENT LOOP TITLE 2 CYCLOPHILIN FROM CAENORHABDITIS ELEGANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLOPHILIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 3, PPIASE, ROTAMASE; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: 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: 562 KEYWDS ISOMERASE(PEPTIDYL-PROLYL CIS-TRANS), ISOMERASE, ROTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR J.DORNAN,A.P.PAGE,P.TAYLOR,S.Y.WU,A.D.WINTER,H.HUSI,M.D.WALKINSHAW REVDAT 5 06-DEC-23 1DYW 1 REMARK REVDAT 4 22-MAY-19 1DYW 1 REMARK REVDAT 3 05-JUL-17 1DYW 1 REMARK REVDAT 2 24-FEB-09 1DYW 1 VERSN REVDAT 1 22-JUN-00 1DYW 0 JRNL AUTH J.DORNAN,A.P.PAGE,P.TAYLOR,S.Y.WU,A.D.WINTER,H.HUSI, JRNL AUTH 2 M.D.WALKINSHAW JRNL TITL BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF A DIVERGENT JRNL TITL 2 LOOP CYCLOPHILIN FROM CAENORHABDITIS ELEGANS JRNL REF J.BIOL.CHEM. V. 274 34877 1999 JRNL REFN ISSN 0021-9258 JRNL PMID 10574961 JRNL DOI 10.1074/JBC.274.49.34877 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.MIKOL,J.KALLEN,G.PFLUEGL,M.D.WALKINSHAW REMARK 1 TITL X-RAY STRUCTURE OF A MONOMERIC CYCLOPHILIN REMARK 1 REF J.MOL.BIOL. V. 234 1119 1993 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 8263916 REMARK 1 DOI 10.1006/JMBI.1993.1664 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.215 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1064 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 20135 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.204 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 934 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 17786 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1296 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 252 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1561.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6247 REMARK 3 NUMBER OF RESTRAINTS : 5295 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.039 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.040 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.019 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE C-TERMINAL RESIDUE WAS NOT SEEN IN REMARK 3 THE DENSITY MAPS REMARK 4 REMARK 4 1DYW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1290004343. 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 : 5.60 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 : ENRAF-NONIUS FR571 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21337 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 6.590 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.27800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.587 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1CWA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPEG5000, SODIUM CITRATE, PH 5.6, PH REMARK 280 5.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 61.56200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.30400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.30400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.78100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.30400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.30400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 92.34300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.30400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.30400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.78100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.30400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.30400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 92.34300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 61.56200 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 300 REMARK: BIOLOGICAL_UNIT: MONOMER 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 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 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 ALA A 173 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 67 -81.28 -142.02 REMARK 500 GLU A 88 -60.06 165.36 REMARK 500 THR A 126 54.03 -115.65 REMARK 500 PHE A 136 11.03 -142.14 REMARK 500 LEU A 171 -62.10 -106.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 448 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A 449 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A 450 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A 451 DISTANCE = 7.17 ANGSTROMS REMARK 525 HOH A 452 DISTANCE = 7.64 ANGSTROMS DBREF 1DYW A 1 173 UNP P52011 CYP3_CAEEL 1 173 SEQRES 1 A 173 MET SER ARG SER LYS VAL PHE PHE ASP ILE THR ILE GLY SEQRES 2 A 173 GLY LYS ALA SER GLY ARG ILE VAL MET GLU LEU TYR ASP SEQRES 3 A 173 ASP VAL VAL PRO LYS THR ALA GLY ASN PHE ARG ALA LEU SEQRES 4 A 173 CYS THR GLY GLU ASN GLY ILE GLY LYS SER GLY LYS PRO SEQRES 5 A 173 LEU HIS PHE LYS GLY SER LYS PHE HIS ARG ILE ILE PRO SEQRES 6 A 173 ASN PHE MET ILE GLN GLY GLY ASP PHE THR ARG GLY ASN SEQRES 7 A 173 GLY THR GLY GLY GLU SER ILE TYR GLY GLU LYS PHE PRO SEQRES 8 A 173 ASP GLU ASN PHE LYS GLU LYS HIS THR GLY PRO GLY VAL SEQRES 9 A 173 LEU SER MET ALA ASN ALA GLY PRO ASN THR ASN GLY SER SEQRES 10 A 173 GLN PHE PHE LEU CYS THR VAL LYS THR GLU TRP LEU ASP SEQRES 11 A 173 GLY LYS HIS VAL VAL PHE GLY ARG VAL VAL GLU GLY LEU SEQRES 12 A 173 ASP VAL VAL LYS ALA VAL GLU SER ASN GLY SER GLN SER SEQRES 13 A 173 GLY LYS PRO VAL LYS ASP CYS MET ILE ALA ASP CYS GLY SEQRES 14 A 173 GLN LEU LYS ALA FORMUL 2 HOH *252(H2 O) HELIX 1 AA1 VAL A 29 GLY A 42 1 14 HELIX 2 AA2 THR A 126 ASP A 130 5 5 HELIX 3 AA3 GLY A 142 SER A 151 1 10 SHEET 1 AA1 8 ARG A 62 ILE A 64 0 SHEET 2 AA1 8 MET A 68 GLY A 71 -1 O GLN A 70 N ARG A 62 SHEET 3 AA1 8 PHE A 119 CYS A 122 -1 O LEU A 121 N ILE A 69 SHEET 4 AA1 8 VAL A 104 MET A 107 -1 N SER A 106 O PHE A 120 SHEET 5 AA1 8 VAL A 135 GLU A 141 -1 O PHE A 136 N LEU A 105 SHEET 6 AA1 8 LYS A 15 LEU A 24 -1 N VAL A 21 O VAL A 140 SHEET 7 AA1 8 LYS A 5 ILE A 12 -1 N VAL A 6 O MET A 22 SHEET 8 AA1 8 CYS A 163 LYS A 172 -1 O LEU A 171 N LYS A 5 CRYST1 60.608 60.608 123.124 90.00 90.00 90.00 P 41 21 2 8 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 0.016499 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016499 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008122 0.00000