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- PDB-2uwi: Structure of CrmE, a poxvirus TNF receptor -

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Basic information

Entry
Database: PDB / ID: 2uwi
TitleStructure of CrmE, a poxvirus TNF receptor
ComponentsCRME PROTEIN
KeywordsRECEPTOR / POXVIRUS TNF RECEPTOR / RECEPTOR IMMUNOMODULATOR / TNF ALPHA RECEPTOR
Function / homology
Function and homology information


tumor necrosis factor receptor activity / regulation of T cell cytokine production / negative regulation of neuroinflammatory response / tumor necrosis factor binding / positive regulation of myelination / positive regulation of membrane protein ectodomain proteolysis / positive regulation of oligodendrocyte differentiation / regulation of T cell proliferation / extrinsic apoptotic signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage
Similarity search - Function
Tumor necrosis factor receptor, N-terminal, viral / : / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsGraham, S.C. / Bahar, M.W. / Abrescia, N.G. / Smith, G.L. / Stuart, D.I. / Grimes, J.M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of Crme, a Virus-Encoded Tumour Necrosis Factor Receptor.
Authors: Graham, S.C. / Bahar, M.W. / Abrescia, N.G. / Smith, G.L. / Stuart, D.I. / Grimes, J.M.
History
DepositionMar 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRME PROTEIN
B: CRME PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,7442
Polymers31,7442
Non-polymers00
Water3,459192
1
A: CRME PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,8721
Polymers15,8721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CRME PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,8721
Polymers15,8721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.380, 56.490, 122.530
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 CRME PROTEIN / CYTOKINE RESPONSE MODIFIER E


Mass: 15872.030 Da / Num. of mol.: 2 / Fragment: CYSTEINE-RICH DOMAINS 1-3, RESIDUES 22-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Strain: LISTER / Plasmid: PDEST14CRME / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLySS / References: UniProt: Q8UYL3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRDS 1-3 OF CRME, C-TERMINAL HIS TAGGED CONSTRUCT.

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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: 2.27 Å3/Da / Density % sol: 45.86 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 NL PROTEIN (6 MG/ML CRME IN 20 MM TRIS 150 MM NACL PH 8.0) AND 100 NL RESERVOIR (0.1 M CITRATE PH 5.0 PLUS 30% W/V PEG 6000) SITTING DROPS AT 20C EQUILIBRATED AGAINST 100 UL RESERVOIRS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: ADSC CCD / Detector: CCD / Date: May 14, 2006 / Details: SILICON TOROIDAL MIRROR COATED WITH RHODIUM
RadiationMonochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 20089 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTERTNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2→39.193 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINED IN BUSTER TNT BETA VERSION 2.1.1 SIDECHAINS OF RESIDUES A 24 (GLN), A52 (LYS), A53 (TYR), A148 (ARG), B24 (GLN), B86 (ASN), B148 (ARG) WERE NOT VISIBLE IN ELECTRON DENSITY AND WERE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 1014 5 %RANDOM
Rwork0.2101 ---
obs-19013 --
Refinement stepCycle: LAST / Resolution: 2→39.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 0 192 2092
Refine LS restraints
Refine-IDType
X-RAY DIFFRACTIONt_bond_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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