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- PDB-4dgd: TRIMCyp cyclophilin domain from Macaca mulatta: H70C mutant -

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Basic information

Entry
Database: PDB / ID: 4dgd
TitleTRIMCyp cyclophilin domain from Macaca mulatta: H70C mutant
ComponentsTRIMCyp
KeywordsISOMERASE / anti-viral protein
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / protein peptidyl-prolyl isomerization / cyclosporin A binding / negative regulation of protein phosphorylation / activation of protein kinase B activity / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / neutrophil chemotaxis / positive regulation of protein secretion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of NF-kappaB transcription factor activity / RING-type E3 ubiquitin transferase / platelet activation / autophagy / platelet aggregation / integrin binding / positive regulation of protein phosphorylation / protein folding / cellular response to oxidative stress / defense response to virus / positive regulation of MAPK cascade / protein ubiquitination / innate immune response / apoptotic process / protein-containing complex / extracellular region / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-box zinc finger / Cyclophilin-like / Cyclophilin / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site ...Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-box zinc finger / Cyclophilin-like / Cyclophilin / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase A / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCaines, M.E.C. / Bichel, K. / Price, A.J. / McEwan, W.A. / James, L.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Diverse HIV viruses are targeted by a conformationally dynamic antiviral.
Authors: Caines, M.E. / Bichel, K. / Price, A.J. / McEwan, W.A. / Towers, G.J. / Willett, B.J. / Freund, S.M. / James, L.C.
History
DepositionJan 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: TRIMCyp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0742
Polymers17,9811
Non-polymers921
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.320, 55.950, 70.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRIMCyp / Peptidyl-prolyl cis-trans isomerase


Mass: 17981.469 Da / Num. of mol.: 1 / Fragment: cyclophilin domain (UNP residues 304-468) / Mutation: H70C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: TRIMCyp / Plasmid: pOPT / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: B0LJC8, UniProt: P62940*PLUS, peptidylprolyl isomerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 25% w/v PEG4000, 8% v/v propan-2-ol, 0.1 M sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.4→43.924 Å / Num. all: 28507 / Num. obs: 28507 / % possible obs: 97.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.98 Å2 / Rsym value: 0.075 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.483.70.3442.21512340470.34496.3
1.48-1.573.80.2453.11454338010.24596.6
1.57-1.673.80.1724.41376636450.17297.6
1.67-1.813.80.1365.21299534320.13697.5
1.81-1.983.70.0957.11176231560.09598.7
1.98-2.213.70.0699.41077828970.06998.7
2.21-2.563.60.0639.9935725940.06399.2
2.56-3.133.40.05610748921870.05698.8
3.13-4.433.50.03915.3594717180.03997.9
4.43-35.4553.40.02621.6355210300.02699.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WLW

2wlw


Resolution: 1.4→43.92 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.166 / WRfactor Rwork: 0.1341 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.922 / SU B: 1.848 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0689 / SU Rfree: 0.0585 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1683 1440 5.1 %RANDOM
Rwork0.1364 ---
obs0.138 28385 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.37 Å2 / Biso mean: 10.5434 Å2 / Biso min: 3.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2--0.87 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.4→43.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1261 0 6 225 1492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221385
X-RAY DIFFRACTIONr_bond_other_d0.0010.02964
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9391864
X-RAY DIFFRACTIONr_angle_other_deg0.90132351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3735181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59324.60363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52615235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.991155
X-RAY DIFFRACTIONr_chiral_restr0.0930.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021592
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02296
X-RAY DIFFRACTIONr_rigid_bond_restr5.55237887
X-RAY DIFFRACTIONr_sphericity_free7.2985225
X-RAY DIFFRACTIONr_sphericity_bonded2.29552315
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 94 -
Rwork0.238 1771 -
all-1865 -
obs--95.06 %

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