HEADER ISOMERASE 25-SEP-06 2IGV TITLE CYCLOPHILIN 3 COMPLEXED WITH DIPEPTIDE SER-PRO COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPIASE, ROTAMASE, CYCLOPHILIN-3; 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; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-5A KEYWDS ISOMERASE, ROTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR D.KAN REVDAT 4 21-FEB-24 2IGV 1 REMARK REVDAT 3 24-FEB-09 2IGV 1 VERSN REVDAT 2 04-SEP-07 2IGV 1 JRNL REVDAT 1 14-AUG-07 2IGV 0 JRNL AUTH M.A.WEAR,D.KAN,A.RABU,M.D.WALKINSHAW JRNL TITL EXPERIMENTAL DETERMINATION OF VAN DER WAALS ENERGIES IN A JRNL TITL 2 BIOLOGICAL SYSTEM. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 46 6453 2007 JRNL REFN ISSN 1433-7851 JRNL PMID 17654646 JRNL DOI 10.1002/ANIE.200702084 REMARK 2 REMARK 2 RESOLUTION. 1.67 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R 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) : 0.196 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 0.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1321 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 25966 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.191 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 0.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 22642 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 : 14 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1458.7 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 7 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 5764 REMARK 3 NUMBER OF RESTRAINTS : 5377 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.044 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.054 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.417 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.059 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL 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 2IGV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039554. 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 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9821 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25969 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 43.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.05000 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) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.28100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% MPEG 5000, 0.1M SODIUM CITRATE, PH REMARK 280 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.0K 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 60.93500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.06200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.06200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.46750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.06200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.06200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 91.40250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.06200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.06200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.46750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.06200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.06200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 91.40250 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 60.93500 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 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: 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 PHE A 7 CB - CG - CD2 ANGL. DEV. = 5.0 DEGREES REMARK 500 PHE A 7 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 19 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 62 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 62 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 PHE A 67 CB - CG - CD1 ANGL. DEV. = 4.5 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 67 -80.41 -148.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 SER A 201 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SER A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PRO A 202 DBREF 2IGV 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 HET SER A 201 8 HET PRO A 202 8 HETNAM SER SERINE HETNAM PRO PROLINE FORMUL 2 SER C3 H7 N O3 FORMUL 3 PRO C5 H9 N O2 FORMUL 4 HOH *151(H2 O) HELIX 1 1 VAL A 29 GLY A 42 1 14 HELIX 2 2 THR A 126 ASP A 130 5 5 HELIX 3 3 GLY A 142 SER A 151 1 10 SHEET 1 A 8 ARG A 62 ILE A 64 0 SHEET 2 A 8 MET A 68 GLY A 71 -1 O MET A 68 N ILE A 64 SHEET 3 A 8 PHE A 119 CYS A 122 -1 O LEU A 121 N ILE A 69 SHEET 4 A 8 VAL A 104 MET A 107 -1 N VAL A 104 O CYS A 122 SHEET 5 A 8 VAL A 135 GLU A 141 -1 O GLY A 137 N LEU A 105 SHEET 6 A 8 LYS A 15 LEU A 24 -1 N VAL A 21 O VAL A 140 SHEET 7 A 8 LYS A 5 ILE A 12 -1 N PHE A 8 O ILE A 20 SHEET 8 A 8 CYS A 163 LEU A 171 -1 O LEU A 171 N LYS A 5 SITE 1 AC1 12 LYS A 56 ALA A 108 ASN A 109 HIS A 133 SITE 2 AC1 12 PRO A 202 HOH A 204 HOH A 205 HOH A 206 SITE 3 AC1 12 HOH A 207 HOH A 209 HOH A 215 HOH A 217 SITE 1 AC2 8 ARG A 62 PHE A 67 GLN A 70 PHE A 120 SITE 2 AC2 8 HIS A 133 SER A 201 HOH A 206 HOH A 212 CRYST1 62.124 62.124 121.870 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 0.016097 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016097 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008205 0.00000