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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
