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- PDB-6bim: Structure of NlpC1 from Trichomonas vaginalis -

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Basic information

Entry
Database: PDB / ID: 6bim
TitleStructure of NlpC1 from Trichomonas vaginalis
ComponentsClan CA, family C40, NlpC/P60 superfamily cysteine peptidasePapain-like protease
KeywordsHYDROLASE / peptidoglycan / peptidase / NlpC protein
Function / homologyBacterial SH3 domain / NlpC/P60 domain profile. / SH3-like domain, bacterial-type / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Papain-like cysteine peptidase superfamily / Clan CA, family C40, NlpC/P60 superfamily cysteine peptidase
Function and homology information
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SIR / Resolution: 1.547 Å
AuthorsPinheiro, J. / Simoes-Barbosa, A. / Goldstone, D.C.
CitationJournal: Mbio / Year: 2018
Title: The ProtozoanTrichomonas vaginalisTargets Bacteria with Laterally Acquired NlpC/P60 Peptidoglycan Hydrolases.
Authors: Pinheiro, J. / Biboy, J. / Vollmer, W. / Hirt, R.P. / Keown, J.R. / Artuyants, A. / Black, M.M. / Goldstone, D.C. / Simoes-Barbosa, A.
History
DepositionNov 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clan CA, family C40, NlpC/P60 superfamily cysteine peptidase


Theoretical massNumber of molelcules
Total (without water)31,9381
Polymers31,9381
Non-polymers00
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.120, 70.060, 79.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-449-

HOH

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Components

#1: Protein Clan CA, family C40, NlpC/P60 superfamily cysteine peptidase / Papain-like protease


Mass: 31937.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_119910 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A2D7D7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Morpheus screen A1

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→29.24 Å / Num. obs: 83416 / % possible obs: 98.8 % / Redundancy: 5.7 % / Rpim(I) all: 0.03 / Net I/σ(I): 14.1
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1744 / Rpim(I) all: 0.112 / % possible all: 81

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SIR / Resolution: 1.547→29.059 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.67
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 2163 4.94 %Random
Rwork0.1539 ---
obs0.155 83416 99.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.547→29.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 0 516 2743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032332
X-RAY DIFFRACTIONf_angle_d0.6763183
X-RAY DIFFRACTIONf_dihedral_angle_d13.2781374
X-RAY DIFFRACTIONf_chiral_restr0.05340
X-RAY DIFFRACTIONf_plane_restr0.004411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5474-1.56560.24471240.20892458X-RAY DIFFRACTION89
1.5656-1.58470.21491260.19762759X-RAY DIFFRACTION99
1.5847-1.60470.22161160.18942695X-RAY DIFFRACTION98
1.6047-1.62590.2361600.18472710X-RAY DIFFRACTION99
1.6259-1.64810.19161300.17192727X-RAY DIFFRACTION99
1.6481-1.67170.22091270.17732740X-RAY DIFFRACTION98
1.6717-1.69660.16021700.16712705X-RAY DIFFRACTION99
1.6966-1.72310.26371350.16382752X-RAY DIFFRACTION99
1.7231-1.75140.21881600.17012693X-RAY DIFFRACTION100
1.7514-1.78160.21731240.16792717X-RAY DIFFRACTION99
1.7816-1.8140.19871210.17232779X-RAY DIFFRACTION100
1.814-1.84880.21241640.17422748X-RAY DIFFRACTION99
1.8488-1.88660.23161330.16962757X-RAY DIFFRACTION100
1.8866-1.92760.19551630.16662716X-RAY DIFFRACTION100
1.9276-1.97240.19841440.17182760X-RAY DIFFRACTION100
1.9724-2.02170.2011440.15972747X-RAY DIFFRACTION100
2.0217-2.07640.18211550.1612746X-RAY DIFFRACTION100
2.0764-2.13750.17771650.15382738X-RAY DIFFRACTION100
2.1375-2.20640.16071690.1522758X-RAY DIFFRACTION100
2.2064-2.28530.16511330.14112756X-RAY DIFFRACTION100
2.2853-2.37670.18661460.14112748X-RAY DIFFRACTION100
2.3767-2.48480.13731300.14452743X-RAY DIFFRACTION100
2.4848-2.61580.17161290.1472770X-RAY DIFFRACTION100
2.6158-2.77950.14151240.14982798X-RAY DIFFRACTION100
2.7795-2.99390.18251490.1492743X-RAY DIFFRACTION100
2.9939-3.29480.14331250.14942784X-RAY DIFFRACTION100
3.2948-3.77070.1481480.14122743X-RAY DIFFRACTION100
3.7707-4.74740.15241480.12362755X-RAY DIFFRACTION100
4.7474-29.06430.16061620.15682747X-RAY DIFFRACTION100

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