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- PDB-4u4j: Crystal structure of Salmonella alpha-2-macroglobulin mutant Y1175G -

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Basic information

Entry
Database: PDB / ID: 4u4j
TitleCrystal structure of Salmonella alpha-2-macroglobulin mutant Y1175G
ComponentsPutative inner membrane lipoprotein
KeywordsHydrolase inhibitor / thioester / protease inhibitor
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 ...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 enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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 23, 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

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Assembly

Deposited unit
A: Putative inner membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)179,9481
Polymers179,9481
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 area69970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)254.240, 82.160, 98.900
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 Putative inner membrane lipoprotein / alpha-2-macroglobulin


Mass: 179948.078 Da / Num. of mol.: 1 / Fragment: UNP residues 19-1644 / Mutation: K98A, K99A, Y1175G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: STM2532 / 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: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2.5% PEG 4000, 0.1 M sodium acetate pH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97939 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.9→58.989 Å / Num. obs: 46790 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 87.07 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.089 / Χ2: 1.114 / Net I/σ(I): 13.97 / Num. measured all: 307501
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
2.9-2.980.8060.9631.9322535340133581.04598.7
2.98-3.060.9090.6812.8123045335033490.738100
3.06-3.150.9280.5473.5122139324032400.592100
3.15-3.240.9590.44.6720759312031180.43499.9
3.24-3.350.9790.2926.0619057305030480.31999.9
3.35-3.470.9820.2447.6920773297629750.264100
3.47-3.60.9890.1879.7919606284328420.202100
3.6-3.740.9910.14711.8818949278127810.16100
3.74-3.910.9920.1214.0317568265126510.13100
3.91-4.10.9940.09916.1915510252625250.108100
4.1-4.320.9960.08120.1816113243024280.08899.9
4.32-4.590.9960.07123.115201228622860.077100
4.59-4.90.9970.06325.1414028215821580.069100
4.9-5.290.9970.06124.9712462200620060.067100
5.29-5.80.9970.06125.2211959189318920.06699.9
5.8-6.480.9970.05925.8711216168916870.06499.9
6.48-7.490.9970.05327.479565152515220.05899.8
7.49-9.170.9980.04530.197631130112980.04999.8
9.17-12.970.9980.04133.386156102010200.045100
12.970.9990.03531.4132296196060.03997.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.53 Å58.99 Å
Translation8.53 Å58.99 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: 2.9→58.989 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2841 2340 5 %
Rwork0.2436 44433 -
obs0.2457 46773 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 264.97 Å2 / Biso mean: 102.84 Å2 / Biso min: 42.64 Å2
Refinement stepCycle: final / Resolution: 2.9→58.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11873 0 0 0 11873
Num. residues----1538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312113
X-RAY DIFFRACTIONf_angle_d0.78716503
X-RAY DIFFRACTIONf_chiral_restr0.0311864
X-RAY DIFFRACTIONf_plane_restr0.0042188
X-RAY DIFFRACTIONf_dihedral_angle_d13.2074462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.95920.41141330.37362525265898
2.9592-3.02350.37971360.331725752711100
3.0235-3.09380.31981360.314425852721100
3.0938-3.17120.37181350.312125712706100
3.1712-3.25690.39621360.301125852721100
3.2569-3.35280.34981360.283225722708100
3.3528-3.4610.29281360.290525852721100
3.461-3.58460.31491370.278126042741100
3.5846-3.72810.33511360.268325862722100
3.7281-3.89780.27111380.257926162754100
3.8978-4.10320.30061370.250426032740100
4.1032-4.36020.27951370.23226152752100
4.3602-4.69680.27651380.2126132751100
4.6968-5.16920.23811400.202726512791100
5.1692-5.91660.251390.224826442783100
5.9166-7.45190.30721410.243826822823100
7.4519-59.00130.23571490.219128212970100

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