HEADER ISOMERASE/ISOMERASE INHIBITOR 24-MAR-04 1VDN TITLE CRYSTAL STRUCTURE OF YEAST CYCLOPHILIN A COMPLEXED WITH ACE-ALA-ALA- TITLE 2 PRO-ALA-7-AMINO-4-METHYLCOUMARIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLOPHILIN A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: (ACE)AAPA(MCM); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-3A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS BETA BARREL, ISOMERASE-ISOMERASE INHIBITOR COMPLEX, ROTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KONNO,T.SHIBANO,K.OKUDAIRA,N.TAKAHASHI REVDAT 4 25-OCT-23 1VDN 1 LINK REVDAT 3 13-JUL-11 1VDN 1 VERSN REVDAT 2 24-FEB-09 1VDN 1 VERSN REVDAT 1 28-JUN-05 1VDN 0 JRNL AUTH M.KONNO,T.SHIBANO,K.OKUDAIRA,N.TAKAHASHI JRNL TITL CRYSTAL STRUCTURE OF YEAST CYCLOPHILIN A COMPLEXED WITH JRNL TITL 2 ACE-ALA-ALA-PRO-ALA-7-AMINO-4-METHYLCOUMARIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.3 REMARK 3 NUMBER OF REFLECTIONS : 17999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1768 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1256 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 188 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.06 REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.07 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.367 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.88 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.903 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000006498. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18099 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : 28.9000 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) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.08000 REMARK 200 R SYM FOR SHELL (I) : 0.08000 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1IST REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, METHANOL, TRIS-HCL, REMARK 280 PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 15.86850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.36800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.00450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.36800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.86850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.00450 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE ACE-ALA-ALA-PRO-ALA-7-AMINO-4-METHYLCOUMARINN IS PEPTIDE-LIKE, REMARK 400 A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: ACE-ALA-ALA-PRO-ALA-7-AMINO-4-METHYLCOUMARINN REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 2 CB 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 58 -80.31 -147.01 REMARK 500 ASN A 69 13.11 -143.66 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 CHAIN B OF (ACE)AAPA(MCM) REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IST RELATED DB: PDB REMARK 900 FREE YEAST CYCLOPHILIN A DBREF 1VDN A 1 162 UNP P14832 CYPH_YEAST 0 161 DBREF 1VDN B 1 6 PDB 1VDN 1VDN 1 6 SEQRES 1 A 162 MET SER GLN VAL TYR PHE ASP VAL GLU ALA ASP GLY GLN SEQRES 2 A 162 PRO ILE GLY ARG VAL VAL PHE LYS LEU TYR ASN ASP ILE SEQRES 3 A 162 VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU CYS THR SEQRES 4 A 162 GLY GLU LYS GLY PHE GLY TYR ALA GLY SER PRO PHE HIS SEQRES 5 A 162 ARG VAL ILE PRO ASP PHE MET LEU GLN GLY GLY ASP PHE SEQRES 6 A 162 THR ALA GLY ASN GLY THR GLY GLY LYS SER ILE TYR GLY SEQRES 7 A 162 GLY LYS PHE PRO ASP GLU ASN PHE LYS LYS HIS HIS ASP SEQRES 8 A 162 ARG PRO GLY LEU LEU SER MET ALA ASN ALA GLY PRO ASN SEQRES 9 A 162 THR ASN GLY SER GLN PHE PHE ILE THR THR VAL PRO CYS SEQRES 10 A 162 PRO TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY GLU VAL SEQRES 11 A 162 VAL ASP GLY TYR ASP ILE VAL LYS LYS VAL GLU SER LEU SEQRES 12 A 162 GLY SER PRO SER GLY ALA THR LYS ALA ARG ILE VAL VAL SEQRES 13 A 162 ALA LYS SER GLY GLU LEU SEQRES 1 B 6 ACE ALA ALA PRO ALA MCM HET ACE B 1 2 HET MCM B 6 13 HETNAM ACE ACETYL GROUP HETNAM MCM 7-AMINO-4-METHYL-CHROMEN-2-ONE HETSYN MCM 7-AMINO-4-METHYLCOUMARIN FORMUL 2 ACE C2 H4 O FORMUL 2 MCM C10 H9 N O2 FORMUL 3 HOH *188(H2 O) HELIX 1 1 VAL A 27 GLY A 40 1 14 HELIX 2 2 CYS A 117 ASP A 121 5 5 HELIX 3 3 GLY A 133 SER A 142 1 10 SHEET 1 A 8 ARG A 53 ILE A 55 0 SHEET 2 A 8 MET A 59 GLY A 62 -1 O GLN A 61 N ARG A 53 SHEET 3 A 8 PHE A 110 THR A 113 -1 O ILE A 112 N LEU A 60 SHEET 4 A 8 LEU A 95 MET A 98 -1 N SER A 97 O PHE A 111 SHEET 5 A 8 VAL A 126 ASP A 132 -1 O PHE A 127 N LEU A 96 SHEET 6 A 8 GLN A 13 LEU A 22 -1 N VAL A 19 O ASP A 132 SHEET 7 A 8 GLN A 3 ALA A 10 -1 N VAL A 8 O ILE A 15 SHEET 8 A 8 ILE A 154 GLU A 161 -1 O LYS A 158 N ASP A 7 LINK C ACE B 1 N ALA B 2 1555 1555 1.33 LINK C ALA B 5 N MCM B 6 1555 1555 1.34 CISPEP 1 ALA B 3 PRO B 4 0 0.53 SITE 1 AC1 23 GLN A 3 VAL A 19 ARG A 53 ILE A 55 SITE 2 AC1 23 ASP A 57 PHE A 58 GLN A 61 ASP A 91 SITE 3 AC1 23 ARG A 92 ALA A 99 ASN A 100 PHE A 111 SITE 4 AC1 23 PRO A 116 LEU A 120 HIS A 124 PRO A 146 SITE 5 AC1 23 HOH A 174 HOH A 175 HOH A 186 HOH A 274 SITE 6 AC1 23 HOH B 54 HOH B 70 HOH B 118 CRYST1 31.737 40.009 112.736 90.00 90.00 90.00 P 21 21 21 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 0.031509 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024994 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008870 0.00000