HEADER ISOMERASE 13-APR-17 5NOW
TITLE STRUCTURE OF CYCLOPHILIN A IN COMPLEX WITH PYRIDINE-3,4-DIAMINE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: PPIASE A,CYCLOPHILIN A,CYCLOSPORIN A-BINDING PROTEIN,
COMPND 5 ROTAMASE A;
COMPND 6 EC: 5.2.1.8;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: PPIA, CYPA;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS LIGAND COMPLEX, BETA BARREL, PROLYL CIS/TRANS ISOMERASE, CYTOSOLIC,
KEYWDS 2 ISOMERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR C.GEORGIOU,I.W.MCNAE,H.IOANNIDIS,M.JULIEN,M.D.WALKINSHAW
REVDAT 3 17-JAN-24 5NOW 1 REMARK
REVDAT 2 16-AUG-17 5NOW 1 JRNL REMARK
REVDAT 1 12-JUL-17 5NOW 0
JRNL AUTH C.GEORGIOU,I.MCNAE,M.WEAR,H.IOANNIDIS,J.MICHEL,M.WALKINSHAW
JRNL TITL PUSHING THE LIMITS OF DETECTION OF WEAK BINDING USING
JRNL TITL 2 FRAGMENT-BASED DRUG DISCOVERY: IDENTIFICATION OF NEW
JRNL TITL 3 CYCLOPHILIN BINDERS.
JRNL REF J. MOL. BIOL. V. 429 2556 2017
JRNL REFN ESSN 1089-8638
JRNL PMID 28673552
JRNL DOI 10.1016/J.JMB.2017.06.016
REMARK 2
REMARK 2 RESOLUTION. 1.48 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0103
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.48
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.03
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 89.5
REMARK 3 NUMBER OF REFLECTIONS : 29517
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.203
REMARK 3 R VALUE (WORKING SET) : 0.202
REMARK 3 FREE R VALUE : 0.219
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1568
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.48
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1596
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.57
REMARK 3 BIN R VALUE (WORKING SET) : 0.2540
REMARK 3 BIN FREE R VALUE SET COUNT : 81
REMARK 3 BIN FREE R VALUE : 0.3250
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1266
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 8
REMARK 3 SOLVENT ATOMS : 157
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.98
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.35000
REMARK 3 B22 (A**2) : -0.46000
REMARK 3 B33 (A**2) : 0.11000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.078
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.076
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.366
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1319 ; 0.021 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 1246 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1771 ; 2.066 ; 1.951
REMARK 3 BOND ANGLES OTHERS (DEGREES): 2880 ; 1.138 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 170 ; 6.392 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 59 ;33.750 ;24.237
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 231 ;12.530 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;12.332 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 182 ; 0.150 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1524 ; 0.012 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 325 ; 0.002 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 666 ; 1.631 ; 1.565
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 667 ; 1.630 ; 1.566
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 831 ; 2.392 ; 2.337
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 832 ; 2.391 ; 2.338
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 653 ; 2.291 ; 1.831
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 654 ; 2.290 ; 1.831
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 938 ; 3.421 ; 2.635
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1529 ; 5.022 ;13.485
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1530 ; 5.020 ;13.488
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : BABINET MODEL WITH MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 5NOW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-APR-17.
REMARK 100 THE DEPOSITION ID IS D_1200002070.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-FEB-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I04-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.920
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, XIA2
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31129
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480
REMARK 200 RESOLUTION RANGE LOW (A) : 23.140
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 89.8
REMARK 200 DATA REDUNDANCY : 6.000
REMARK 200 R MERGE (I) : 0.08000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52
REMARK 200 COMPLETENESS FOR SHELL (%) : 66.8
REMARK 200 DATA REDUNDANCY IN SHELL : 4.30
REMARK 200 R MERGE FOR SHELL (I) : 0.56000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 5LUD
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.36
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, TRIS-HCL, PH 8.0, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 279.15K
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 21.38500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.48500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.33500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.48500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.38500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.33500
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 7590 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL
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 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 60 -77.28 -141.34
REMARK 500 ASN A 71 8.33 -150.16
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 L89 A 201
DBREF 5NOW A 1 165 UNP P62937 PPIA_HUMAN 1 165
SEQRES 1 A 165 MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL ASP
SEQRES 2 A 165 GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE ALA
SEQRES 3 A 165 ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU
SEQRES 4 A 165 SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER CYS
SEQRES 5 A 165 PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY GLY
SEQRES 6 A 165 ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE
SEQRES 7 A 165 TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU LYS
SEQRES 8 A 165 HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA GLY
SEQRES 9 A 165 PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ALA
SEQRES 10 A 165 LYS THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY
SEQRES 11 A 165 LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET GLU
SEQRES 12 A 165 ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS ILE
SEQRES 13 A 165 THR ILE ALA ASP CYS GLY GLN LEU GLU
HET L89 A 201 8
HETNAM L89 PYRIDINE-3,4-DIAMINE
FORMUL 2 L89 C5 H7 N3
FORMUL 3 HOH *157(H2 O)
HELIX 1 AA1 VAL A 29 GLY A 42 1 14
HELIX 2 AA2 THR A 119 ASP A 123 5 5
HELIX 3 AA3 GLY A 135 PHE A 145 1 11
SHEET 1 AA1 8 ARG A 55 ILE A 57 0
SHEET 2 AA1 8 MET A 61 GLY A 64 -1 O GLN A 63 N ARG A 55
SHEET 3 AA1 8 PHE A 112 CYS A 115 -1 O ILE A 114 N CYS A 62
SHEET 4 AA1 8 ILE A 97 MET A 100 -1 N ILE A 97 O CYS A 115
SHEET 5 AA1 8 VAL A 128 VAL A 132 -1 O PHE A 129 N LEU A 98
SHEET 6 AA1 8 GLU A 15 LEU A 24 -1 N GLU A 23 O LYS A 131
SHEET 7 AA1 8 THR A 5 VAL A 12 -1 N ILE A 10 O LEU A 17
SHEET 8 AA1 8 ILE A 156 LEU A 164 -1 O ASP A 160 N ASP A 9
SITE 1 AC1 8 GLY A 72 ASN A 102 THR A 107 GLY A 109
SITE 2 AC1 8 GLN A 111 HOH A 324 HOH A 368 HOH A 386
CRYST1 42.770 54.670 86.970 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 0.023381 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018292 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011498 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
