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- PDB-2wlw: Structure of the N-terminal capsid domain of HIV-2 -

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Basic information

Entry
Database: PDB / ID: 2wlw
TitleStructure of the N-terminal capsid domain of HIV-2
ComponentsPEPTIDYL-PROLYL CIS-TRANS ISOMERASE
KeywordsISOMERASE / ROTAMASE / RHESUS MACAQUE TRIM-CYP
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 / platelet activation / platelet aggregation / integrin binding / positive regulation of protein phosphorylation / protein folding / cellular response to oxidative stress / positive regulation of MAPK cascade / apoptotic process / protein-containing complex / extracellular region / nucleus / cytoplasm / cytosol
Similarity search - Function
Cyclophilin-like / Cyclophilin / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesMACACA MULATTA (Rhesus monkey)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.5 Å
AuthorsPrice, A.J. / Marzetta, F. / Lammers, M. / Ylinen, L.M.J. / Schaller, T. / Wilson, S.J. / Towers, G.J. / James, L.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Active Site Remodelling Switches HIV Specificity of Antiretroviral Trimcyp
Authors: Price, A.J. / Marzetta, F. / Lammers, M. / Ylinen, L.M.J. / Schaller, T. / Wilson, S.J. / Towers, G.J. / James, L.C.
History
DepositionJun 26, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE


Theoretical massNumber of molelcules
Total (without water)18,0161
Polymers18,0161
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.880, 51.120, 75.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE / TRIM-CYP


Mass: 18016.473 Da / Num. of mol.: 1 / Fragment: CYPA DOMAIN, RESIDUES 46-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MACACA MULATTA (Rhesus monkey) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: B1P761, UniProt: P62940*PLUS, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.61 Å3/Da / Density % sol: 23.18 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→41 Å / Num. obs: 23059 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.2

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Processing

SoftwareName: REFMAC / Version: 5.5.0088 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.5→88.57 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.322 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.1858 5669 5.03 %
Rwork0.154 --
obs0.156 23059 99.791 %
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 16.659 Å2
Baniso -1Baniso -2Baniso -3
1-0.329 Å20 Å20 Å2
2---0.585 Å20 Å2
3---0.256 Å2
Refinement stepCycle: LAST / Resolution: 1.5→88.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 0 207 1463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0222520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4381.9433458
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5845322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65824.219128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7415419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0921522
X-RAY DIFFRACTIONr_chiral_restr0.1590.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212906
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3480.27930
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2430.21168
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3590.2308
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9481.58182
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.82212714
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.01634478
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.9044.53872
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 435 -
Rwork0.244 7816 -
obs--99.47 %

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