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- PDB-4u48: Crystal structure of Salmonella alpha-2-macroglobulin -

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Basic information

Entry
Database: PDB / ID: 4u48
TitleCrystal structure of Salmonella alpha-2-macroglobulin
ComponentsPutative inner membrane lipoprotein
KeywordsHYDROLASE INHIBITOR / thioester / protease inhibitor / unknown function
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 enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 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 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_seq_map_depositor_info ...pdbx_data_processing_status / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative inner membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)181,1801
Polymers181,1801
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area70280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)255.550, 82.180, 99.180
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: 181179.656 Da / Num. of mol.: 1 / Fragment: UNP residues 19-1644 / Mutation: K98A, K99A
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: 57.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 4% 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: ID29 / Wavelength: 0.97939 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.95→56.707 Å / Num. obs: 44869 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 74.82 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.119 / Χ2: 1.081 / Net I/σ(I): 11.06 / Num. measured all: 524432
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.95-3.030.8560.7532.0136317622061410.82498.7
3.03-3.110.9190.5782.7939461615061480.629100
3.11-3.20.9420.4693.4638227598659860.511100
3.2-3.30.9670.364.4336743582758250.393100
3.3-3.410.9770.2725.6734444559855980.298100
3.41-3.530.9820.2256.530225534953490.248100
3.53-3.660.9880.1878.2232726525852560.204100
3.66-3.810.9910.15910.0333238505950580.172100
3.81-3.980.9920.13311.7631337481548150.145100
3.98-4.170.9940.11613.6629701463846380.126100
4.17-4.40.9940.09815.8427472436843670.107100
4.4-4.660.9950.08917.6225403415841560.097100
4.66-4.990.9960.07918.0422581391939180.087100
4.99-5.390.9940.0817.5519672363536310.08999.9
5.39-5.90.9950.08219.0621328332733270.089100
5.9-6.60.9960.0819.3919539302230220.087100
6.6-7.620.9960.0721.6316771267126710.076100
7.62-9.330.9970.05823.8313184224022400.063100
9.33-13.190.9970.05326.169920173517350.058100
13.190.9970.05428.2261439619490.05998.8

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.74 / FOM acentric: 0.75 / FOM centric: 0.66 / Reflection: 44866 / Reflection acentric: 40026 / Reflection centric: 4840
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.4-56.7070.90.920.8321031532571
5.3-8.40.830.860.6561095181928
4.2-5.30.840.860.7175466684862
3.7-4.20.790.80.6875246794730
3.2-3.70.70.710.6113350122271123
3-3.20.560.570.4982347608626

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
RESOLVE2.15model building
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.14data extraction
SOLVEphasing
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.95→56.707 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 2243 5 %
Rwork0.2244 42603 -
obs0.2265 44846 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 288 Å2 / Biso mean: 95.8363 Å2 / Biso min: 36.62 Å2
Refinement stepCycle: final / Resolution: 2.95→56.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11880 0 0 0 11880
Num. residues----1538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312121
X-RAY DIFFRACTIONf_angle_d0.75116515
X-RAY DIFFRACTIONf_chiral_restr0.031865
X-RAY DIFFRACTIONf_plane_restr0.0042187
X-RAY DIFFRACTIONf_dihedral_angle_d10.8654464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9501-3.01420.40641370.343826092746
3.0142-3.08430.34251370.303325912728
3.0843-3.16150.35171390.284526372776
3.1615-3.24690.33911370.265126072744
3.2469-3.34250.31461370.256826182755
3.3425-3.45030.31581390.258726442783
3.4503-3.57360.29811410.247826622803
3.5736-3.71670.31951380.233426212759
3.7167-3.88580.28391380.231126352773
3.8858-4.09060.27171410.226326632804
4.0906-4.34680.25961400.203626602800
4.3468-4.68230.21151400.192226622802
4.6823-5.15320.22091420.182626952837
5.1532-5.89820.26611410.202826952836
5.8982-7.42850.24821440.230227332877
7.4285-56.7170.22691520.21528713023

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