HEADER ISOMERASE 19-APR-01 1IHG TITLE BOVINE CYCLOPHILIN 40, MONOCLINIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLOPHILIN 40; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 40 KDA PEPTIDYL-PROLYL CIS-TRANS ISOMERASE; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS PPIASE IMMUNOPHILIN TETRATRICOPEPTIDE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.TAYLOR,J.DORNAN,A.CARRELLO,R.F.MINCHIN,T.RATAJCZAK,M.D.WALKINSHAW REVDAT 5 03-APR-24 1IHG 1 REMARK REVDAT 4 07-FEB-24 1IHG 1 REMARK REVDAT 3 13-JUL-11 1IHG 1 VERSN REVDAT 2 24-FEB-09 1IHG 1 VERSN REVDAT 1 16-MAY-01 1IHG 0 JRNL AUTH P.TAYLOR,J.DORNAN,A.CARRELLO,R.F.MINCHIN,T.RATAJCZAK, JRNL AUTH 2 M.D.WALKINSHAW JRNL TITL TWO STRUCTURES OF CYCLOPHILIN 40: FOLDING AND FIDELITY IN JRNL TITL 2 THE TPR DOMAINS. JRNL REF STRUCTURE V. 9 431 2001 JRNL REFN ISSN 0969-2126 JRNL PMID 11377203 JRNL DOI 10.1016/S0969-2126(01)00603-7 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) : 24.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 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) : 0.178 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.178 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2035 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 38413 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.176 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 37387 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2810 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 489 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3305.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 13223 REMARK 3 NUMBER OF RESTRAINTS : 11467 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.000 REMARK 3 ANGLE DISTANCES (A) : 0.020 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.025 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.030 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.040 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.070 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 1IHG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013270. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41259 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 28.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6700 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 (%) : 87.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.87 REMARK 200 R MERGE FOR SHELL (I) : 0.09600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.030 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: CYCLOPHILIN A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, MES GLYCEROL SODIUM REMARK 280 CHLORIDE, PH 6.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 63.06250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.66400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 63.06250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.66400 REMARK 290 SMTRY3 4 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 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 MET A 1 REMARK 465 ALA A 366 REMARK 465 LYS A 367 REMARK 465 MET A 368 REMARK 465 PHE A 369 REMARK 465 ALA A 370 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 49 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 PHE A 132 CB - CG - CD2 ANGL. DEV. = 4.8 DEGREES REMARK 500 PHE A 132 CB - CG - CD1 ANGL. DEV. = -5.0 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 80 -75.27 -144.42 REMARK 500 ASN A 91 13.61 -145.47 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 GOL A 371 DBREF 1IHG A 1 370 UNP P26882 PPID_BOVIN 1 370 SEQRES 1 A 370 MET SER HIS PRO SER PRO GLN ALA LYS PRO SER ASN PRO SEQRES 2 A 370 SER ASN PRO ARG VAL PHE PHE ASP VAL ASP ILE GLY GLY SEQRES 3 A 370 GLU ARG VAL GLY ARG ILE VAL LEU GLU LEU PHE ALA ASP SEQRES 4 A 370 ILE VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU CYS SEQRES 5 A 370 THR GLY GLU LYS GLY ILE GLY PRO THR THR GLY LYS PRO SEQRES 6 A 370 LEU HIS PHE LYS GLY CYS PRO PHE HIS ARG ILE ILE LYS SEQRES 7 A 370 LYS PHE MET ILE GLN GLY GLY ASP PHE SER ASN GLN ASN SEQRES 8 A 370 GLY THR GLY GLY GLU SER ILE TYR GLY GLU LYS PHE GLU SEQRES 9 A 370 ASP GLU ASN PHE HIS TYR LYS HIS ASP LYS GLU GLY LEU SEQRES 10 A 370 LEU SER MET ALA ASN ALA GLY SER ASN THR ASN GLY SER SEQRES 11 A 370 GLN PHE PHE ILE THR THR VAL PRO THR PRO HIS LEU ASP SEQRES 12 A 370 GLY LYS HIS VAL VAL PHE GLY GLN VAL ILE LYS GLY MET SEQRES 13 A 370 GLY VAL ALA LYS ILE LEU GLU ASN VAL GLU VAL LYS GLY SEQRES 14 A 370 GLU LYS PRO ALA LYS LEU CYS VAL ILE ALA GLU CYS GLY SEQRES 15 A 370 GLU LEU LYS GLU GLY ASP ASP TRP GLY ILE PHE PRO LYS SEQRES 16 A 370 ASP GLY SER GLY ASP SER HIS PRO ASP PHE PRO GLU ASP SEQRES 17 A 370 ALA ASP VAL ASP LEU LYS ASP VAL ASP LYS ILE LEU LEU SEQRES 18 A 370 ILE SER GLU ASP LEU LYS ASN ILE GLY ASN THR PHE PHE SEQRES 19 A 370 LYS SER GLN ASN TRP GLU MET ALA ILE LYS LYS TYR THR SEQRES 20 A 370 LYS VAL LEU ARG TYR VAL GLU GLY SER ARG ALA ALA ALA SEQRES 21 A 370 GLU ASP ALA ASP GLY ALA LYS LEU GLN PRO VAL ALA LEU SEQRES 22 A 370 SER CYS VAL LEU ASN ILE GLY ALA CYS LYS LEU LYS MET SEQRES 23 A 370 SER ASP TRP GLN GLY ALA VAL ASP SER CYS LEU GLU ALA SEQRES 24 A 370 LEU GLU ILE ASP PRO SER ASN THR LYS ALA LEU TYR ARG SEQRES 25 A 370 ARG ALA GLN GLY TRP GLN GLY LEU LYS GLU TYR ASP GLN SEQRES 26 A 370 ALA LEU ALA ASP LEU LYS LYS ALA GLN GLU ILE ALA PRO SEQRES 27 A 370 GLU ASP LYS ALA ILE GLN ALA GLU LEU LEU LYS VAL LYS SEQRES 28 A 370 GLN LYS ILE LYS ALA GLN LYS ASP LYS GLU LYS ALA ALA SEQRES 29 A 370 TYR ALA LYS MET PHE ALA HET GOL A 371 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *489(H2 O) HELIX 1 1 VAL A 41 GLY A 54 1 14 HELIX 2 2 THR A 139 ASP A 143 5 5 HELIX 3 3 GLY A 155 ASN A 164 1 10 HELIX 4 4 PHE A 205 ALA A 209 5 5 HELIX 5 5 ASP A 215 SER A 236 1 22 HELIX 6 6 ASN A 238 ALA A 260 1 23 HELIX 7 7 GLU A 261 ALA A 266 1 6 HELIX 8 8 LEU A 268 MET A 286 1 19 HELIX 9 9 ASP A 288 GLU A 301 1 14 HELIX 10 10 ASN A 306 LEU A 320 1 15 HELIX 11 11 GLU A 322 ALA A 337 1 16 HELIX 12 12 ASP A 340 ALA A 363 1 24 SHEET 1 A 8 PHE A 73 ILE A 77 0 SHEET 2 A 8 MET A 81 GLY A 84 -1 O MET A 81 N ILE A 77 SHEET 3 A 8 PHE A 132 THR A 135 -1 O PHE A 132 N GLY A 84 SHEET 4 A 8 LEU A 117 MET A 120 -1 O LEU A 117 N THR A 135 SHEET 5 A 8 VAL A 148 LYS A 154 -1 N PHE A 149 O LEU A 118 SHEET 6 A 8 GLU A 27 LEU A 36 -1 O VAL A 33 N ILE A 153 SHEET 7 A 8 ARG A 17 ILE A 24 -1 O VAL A 18 N LEU A 34 SHEET 8 A 8 CYS A 176 LEU A 184 -1 N VAL A 177 O ASP A 23 SHEET 1 B 2 VAL A 167 LYS A 168 0 SHEET 2 B 2 LYS A 171 PRO A 172 -1 O LYS A 171 N LYS A 168 CISPEP 1 LYS A 9 PRO A 10 0 3.36 SITE 1 AC1 8 PHE A 205 PRO A 206 GLU A 207 ARG A 251 SITE 2 AC1 8 HOH A 411 HOH A 420 HOH A 745 HOH A 884 CRYST1 126.125 47.328 85.563 90.00 119.42 90.00 C 1 2 1 4 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 0.007929 0.000000 0.004471 0.00000 SCALE2 0.000000 0.021129 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013418 0.00000