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- PDB-6j91: Structure of a hypothetical protease -

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Basic information

Entry
Database: PDB / ID: 6j91
TitleStructure of a hypothetical protease
Components
  • Small vasohibin-binding protein
  • Tubulinyl-Tyr carboxypeptidase 1
KeywordsPEPTIDE BINDING PROTEIN/HYDROLASE / protease / complex / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Carboxyterminal post-translational modifications of tubulin / regulation of cellular senescence / negative regulation of lymphangiogenesis / peptidase activator activity / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / axon development ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Carboxyterminal post-translational modifications of tubulin / regulation of cellular senescence / negative regulation of lymphangiogenesis / peptidase activator activity / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / axon development / negative regulation of endothelial cell proliferation / negative regulation of blood vessel endothelial cell migration / protein secretion / regulation of angiogenesis / metallocarboxypeptidase activity / negative regulation of protein ubiquitination / negative regulation of angiogenesis / response to wounding / apical part of cell / actin binding / microtubule binding / angiogenesis / cytoskeleton / regulation of cell cycle / cell cycle / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Tubulinyl-Tyr carboxypeptidase / Small vasohibin-binding protein / Vasohibin / Coiled-coil domain-containing protein 23
Similarity search - Domain/homology
Tubulinyl-Tyr carboxypeptidase 1 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsLiao, S. / Gao, J. / Xu, C.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31500601 China
National Natural Science Foundation of China31570737 China
National Natural Science Foundation of China31770806 China
CitationJournal: Cell Res. / Year: 2019
Title: Molecular basis of vasohibins-mediated detyrosination and its impact on spindle function and mitosis.
Authors: Liao, S. / Rajendraprasad, G. / Wang, N. / Eibes, S. / Gao, J. / Yu, H. / Wu, G. / Tu, X. / Huang, H. / Barisic, M. / Xu, C.
History
DepositionJan 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small vasohibin-binding protein
B: Tubulinyl-Tyr carboxypeptidase 1


Theoretical massNumber of molelcules
Total (without water)36,0062
Polymers36,0062
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-12 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.234, 123.363, 129.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Small vasohibin-binding protein / Coiled coil domain-containing protein 23


Mass: 7962.624 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SVBP, CCDC23
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8N300
#2: Protein Tubulinyl-Tyr carboxypeptidase 1 / / Tubulin carboxypeptidase 1 / Tyrosine carboxypeptidase 1 / TTCP 1 / Vasohibin-1


Mass: 28043.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VASH1, KIAA1036, VASH
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase

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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: 3.84 Å3/Da / Density % sol: 67.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Na citrate tribasic dihydrate pH 5.5, 16% PEG 8000, 0.01M Cadmium chloride hydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 7492 / % possible obs: 100 % / Redundancy: 30.3 % / Rpim(I) all: 0.053 / Net I/σ(I): 18.9
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 30.1 % / Num. unique obs: 353 / Rpim(I) all: 0.134 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 3.5→44.664 Å / SU ML: 0.44 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 355 4.94 %
Rwork0.2322 --
obs0.2336 7187 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→44.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 0 0 2117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022167
X-RAY DIFFRACTIONf_angle_d0.6122923
X-RAY DIFFRACTIONf_dihedral_angle_d14.2521326
X-RAY DIFFRACTIONf_chiral_restr0.044313
X-RAY DIFFRACTIONf_plane_restr0.004376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5001-4.00630.27061230.23252227X-RAY DIFFRACTION100
4.0063-5.04640.22731330.21232235X-RAY DIFFRACTION100
5.0464-44.66720.2856990.24852370X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 3.6461 Å / Origin y: 21.1326 Å / Origin z: 20.8818 Å
111213212223313233
T0.2755 Å2-0.0575 Å20.088 Å2-0.4213 Å2-0.0657 Å2--0.3088 Å2
L1.7539 °2-0.1162 °20.379 °2-2.539 °20.4367 °2--2.5334 °2
S0.127 Å °-0.2295 Å °0.2965 Å °0.2951 Å °0.1256 Å °-0.0207 Å °-0.034 Å °0.0482 Å °-0.2343 Å °
Refinement TLS groupSelection details: all

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