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- PDB-3nvx: Molecular mechanism of guidance cue recognition -

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Basic information

Entry
Database: PDB / ID: 3nvx
TitleMolecular mechanism of guidance cue recognition
ComponentsProtein A39
KeywordsVIRAL PROTEIN / Beta-Propeller
Function / homology
Function and homology information


semaphorin receptor binding / extracellular region
Similarity search - Function
Semaphorin / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Semaphorin-like protein A39
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsLiu, H. / Juo, Z. / Shim, A. / Focia, P. / Chen, X. / Garcia, C. / He, X.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Structural Basis of Semaphorin-Plexin Recognition and Viral Mimicry from Sema7A and A39R Complexes with PlexinC1.
Authors: Liu, H. / Juo, Z.S. / Shim, A.H. / Focia, P.J. / Chen, X. / Garcia, K.C. / He, X.
History
DepositionJul 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein A39
B: Protein A39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1764
Polymers86,7342
Non-polymers4422
Water15,529862
1
A: Protein A39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5882
Polymers43,3671
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein A39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5882
Polymers43,3671
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.088, 171.006, 211.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein A39


Mass: 43366.859 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 15-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Copenhagen / Gene: A39R / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P21062
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 862 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2M Li2SO4, 15% PEG3350, 20% Glycerol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-3 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 63111 / Num. obs: 62229 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2374 / % possible all: 91.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2→47.686 Å / SU ML: 0.26 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 3154 5.07 %RANDOM
Rwork0.1758 ---
obs0.1782 62224 98.61 %-
all-63101 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.238 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0635 Å2-0 Å20 Å2
2---2.2339 Å2-0 Å2
3---5.2973 Å2
Refinement stepCycle: LAST / Resolution: 2→47.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5966 0 28 862 6856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076139
X-RAY DIFFRACTIONf_angle_d1.0538302
X-RAY DIFFRACTIONf_dihedral_angle_d16.4072234
X-RAY DIFFRACTIONf_chiral_restr0.069921
X-RAY DIFFRACTIONf_plane_restr0.0051052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02990.31861010.2392374X-RAY DIFFRACTION90
2.0299-2.06160.29351500.22342330X-RAY DIFFRACTION93
2.0616-2.09540.21461130.21312474X-RAY DIFFRACTION96
2.0954-2.13150.28191380.20792472X-RAY DIFFRACTION95
2.1315-2.17030.26731520.21932474X-RAY DIFFRACTION98
2.1703-2.2120.26931570.20622508X-RAY DIFFRACTION99
2.212-2.25720.25431200.18792538X-RAY DIFFRACTION99
2.2572-2.30630.26251490.17822563X-RAY DIFFRACTION100
2.3063-2.35990.25341420.18232574X-RAY DIFFRACTION100
2.3599-2.41890.24421290.18192607X-RAY DIFFRACTION100
2.4189-2.48430.25871150.18722590X-RAY DIFFRACTION100
2.4843-2.55740.26141300.18492639X-RAY DIFFRACTION100
2.5574-2.640.1981310.17632561X-RAY DIFFRACTION100
2.64-2.73430.2261450.1672566X-RAY DIFFRACTION100
2.7343-2.84380.21011610.16752595X-RAY DIFFRACTION100
2.8438-2.97320.21521220.17022627X-RAY DIFFRACTION100
2.9732-3.12990.21421330.16972579X-RAY DIFFRACTION100
3.1299-3.3260.23181500.1692610X-RAY DIFFRACTION100
3.326-3.58270.20161310.15322647X-RAY DIFFRACTION100
3.5827-3.94310.19871510.1542618X-RAY DIFFRACTION100
3.9431-4.51330.19171150.13792669X-RAY DIFFRACTION100
4.5133-5.68470.16771550.13782680X-RAY DIFFRACTION100
5.6847-47.69940.21221640.19652775X-RAY DIFFRACTION100

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