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- PDB-2ose: Crystal Structure of the Mimivirus Cyclophilin -

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Basic information

Entry
Database: PDB / ID: 2ose
TitleCrystal Structure of the Mimivirus Cyclophilin
ComponentsProbable peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / mimivirus / cyclophilin
Function / homology
Function and homology information


virion component => GO:0044423 / peptidyl-prolyl cis-trans isomerase activity / host cell cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Structural PPIase-like protein L605
Similarity search - Component
Biological speciesMimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsEisenmesser, E.Z. / Thai, V. / Renesto, P. / Raoult, D.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus.
Authors: Thai, V. / Renesto, P. / Fowler, C.A. / Brown, D.J. / Davis, T. / Gu, W. / Pollock, D.D. / Kern, D. / Raoult, D. / Eisenmesser, E.Z.
History
DepositionFeb 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6423
Polymers26,5711
Non-polymers712
Water1,38777
1
A: Probable peptidyl-prolyl cis-trans isomerase
hetero molecules

A: Probable peptidyl-prolyl cis-trans isomerase
hetero molecules

A: Probable peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9259
Polymers79,7133
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area4560 Å2
ΔGint-67.9 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.032, 95.032, 95.032
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
DetailsThe biological assembly is possibly a trimer generated from the monomer in the asymmetric unit by the operations: Z,X,Y and Y,Z,X

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Components

#1: Protein Probable peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase


Mass: 26570.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mimivirus / Genus: Mimivirus / Gene: MIMI_L605 / Plasmid: pET15-B / Production host: Escherichia coli (E. coli) / References: UniProt: Q5UP71, peptidylprolyl isomerase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium phosphate monobasic monohydrate, 0.1 M potassium phosphate monobasic, 0.1 M MES monohydrate (pH 6.5), and 2 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 30, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→67.27 Å / Num. all: 18528 / Num. obs: 18528 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Rmerge(I) obs: 0.067 / Χ2: 0.988 / Net I/σ(I): 10.3
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.712 / Num. unique all: 1836 / Χ2: 0.938 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å14.84 Å
Translation3 Å14.84 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BIT

2bit


Resolution: 2.04→67.27 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.075 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 948 5.1 %RANDOM
Rwork0.214 ---
obs0.216 18485 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.792 Å2
Refinement stepCycle: LAST / Resolution: 2.04→67.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 2 77 1637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221593
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9682158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7065192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55924.19881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22215260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8571510
X-RAY DIFFRACTIONr_chiral_restr0.1120.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021240
X-RAY DIFFRACTIONr_nbd_refined0.2060.2643
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21065
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.27
X-RAY DIFFRACTIONr_mcbond_it1.1961.51003
X-RAY DIFFRACTIONr_mcangle_it1.81221565
X-RAY DIFFRACTIONr_scbond_it2.4833683
X-RAY DIFFRACTIONr_scangle_it3.74.5593
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 61 -
Rwork0.246 1273 -
obs-1334 100 %

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