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- PDB-4u59: Crystal structure of Salmonella alpha-2-macroglobulin reacted wit... -

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Basic information

Entry
Database: PDB / ID: 4u59
TitleCrystal structure of Salmonella alpha-2-macroglobulin reacted with methylamine
Componentsalpha-2-macroglobulin
KeywordsHYDROLASE INHIBITOR / macroglobulin / thioester / protease inhibitor / methylamine
Function / homology
Function and homology information


endopeptidase inhibitor activity / extracellular space / plasma membrane
Similarity search - Function
Alpha-2-macroglobulin MG3 domain / Alpha-2-macroglobulin, bacteria / Alpha-2-macroglobulin, MG1 domain / Bacterial Alpha-2-macroglobulin, MG5 domain / Bacterial alpha-2-macroglobulin MG10 domain / Bacterial Alpha-2-macroglobulin, MG6 domain / : / : / Bacterial alpha-2-macroglobulin MG3 domain / Bacterial macroglobulin domain 6 ...Alpha-2-macroglobulin MG3 domain / Alpha-2-macroglobulin, bacteria / Alpha-2-macroglobulin, MG1 domain / Bacterial Alpha-2-macroglobulin, MG5 domain / Bacterial alpha-2-macroglobulin MG10 domain / Bacterial Alpha-2-macroglobulin, MG6 domain / : / : / Bacterial alpha-2-macroglobulin MG3 domain / Bacterial macroglobulin domain 6 / Bacterial Alpha-2-macroglobulin MG1 domain / Bacterial Alpha-2-macroglobulin MG5 domain / Bacterial Alpha-2-macroglobulin MG10 domain / Bacterial alpha-2 macroglobulin MG2 domain / A2MG, CUB domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Alpha-2-macroglobulin
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.09 Å
AuthorsWong, S.G. / Dessen, A.
Funding support France, 1items
OrganizationGrant numberCountry
FINOVI France
CitationJournal: Nat Commun / Year: 2014
Title: Structure of a bacterial alpha 2-macroglobulin reveals mimicry of eukaryotic innate immunity.
Authors: Wong, S.G. / Dessen, A.
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha-2-macroglobulin


Theoretical massNumber of molelcules
Total (without water)180,0681
Polymers180,0681
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area69840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)254.960, 82.230, 98.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein alpha-2-macroglobulin


Mass: 180068.234 Da / Num. of mol.: 1 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: CY43_13515 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZN46

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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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 7% PEG 4000, 0.1 M sodium acetate pH 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.09→50.732 Å / Num. obs: 39003 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 75.26 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.145 / Χ2: 0.985 / Net I/σ(I): 13.38 / Num. measured all: 289600
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.09-3.170.7651.1322.0521629285128511.215100
3.17-3.260.8520.8772.6720869275527550.941100
3.26-3.350.9370.6243.6720279268226820.67100
3.35-3.450.9410.5214.319804262526250.559100
3.45-3.570.9680.3935.6719393256625660.422100
3.57-3.690.9690.3276.6318459245124510.351100
3.69-3.830.9820.2638.0217741235923590.283100
3.83-3.990.9870.20410.0417300231023100.22100
3.99-4.170.9910.16511.9416485221022090.178100
4.17-4.370.9950.12315.2815604210221020.133100
4.37-4.610.9960.10217.9714938202520250.11100
4.61-4.890.9970.08320.9113961189418940.09100
4.89-5.220.9970.08221.4713311181118110.088100
5.22-5.640.9970.08520.4912346167216720.091100
5.64-6.180.9970.08619.9211506156415640.093100
6.18-6.910.9970.07622.0310329141614160.082100
6.91-7.980.9980.05429.019140126812680.058100
7.98-9.770.9990.03440.457602107910790.037100
9.77-13.820.9990.02947.1858898678660.03299.9
13.820.9990.02747.2330155154980.0396.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8 Å56.65 Å
Translation8 Å56.65 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U48

4u48


Resolution: 3.09→50.732 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 1951 5 %
Rwork0.2314 37035 -
obs0.2339 38986 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.56 Å2 / Biso mean: 88.1098 Å2 / Biso min: 27.83 Å2
Refinement stepCycle: final / Resolution: 3.09→50.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11882 0 0 0 11882
Num. residues----1538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312123
X-RAY DIFFRACTIONf_angle_d0.68416517
X-RAY DIFFRACTIONf_chiral_restr0.0281865
X-RAY DIFFRACTIONf_plane_restr0.0032189
X-RAY DIFFRACTIONf_dihedral_angle_d10.414464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.0901-3.16730.39931390.348626152754
3.1673-3.2530.35991360.306825752711
3.253-3.34870.37411360.275626002736
3.3487-3.45670.38211370.278326082745
3.4567-3.58030.28221390.246126382777
3.5803-3.72360.2831360.245125862722
3.7236-3.8930.3171390.244126442783
3.893-4.09810.27621380.235326132751
4.0981-4.35480.24831380.204826302768
4.3548-4.69080.23211390.190326362775
4.6908-5.16240.25261410.185426722813
5.1624-5.90850.23391400.209426722812
5.9085-7.44030.27761430.257427072850
7.4403-50.7390.28241500.223328392989

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