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- PDB-4rtd: Escherichia coli alpha-2-macroglobulin activated by porcine elastase -

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Basic information

Entry
Database: PDB / ID: 4rtd
TitleEscherichia coli alpha-2-macroglobulin activated by porcine elastase
ComponentsUncharacterized lipoprotein YfhM
KeywordsLIPID BINDING PROTEIN / thioester domain / macroglobulin
Function / homology
Function and homology information


endopeptidase inhibitor activity / protein homodimerization 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.65 Å
AuthorsFyfe, C.D. / Grinter, R. / Roszak, A.W. / Josts, I. / Cogdell, R.J. / Walker, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of protease-cleaved Escherichia coli alpha-2-macroglobulin reveals a putative mechanism of conformational activation for protease entrapment.
Authors: Fyfe, C.D. / Grinter, R. / Josts, I. / Mosbahi, K. / Roszak, A.W. / Cogdell, R.J. / Wall, D.M. / Burchmore, R.J. / Byron, O. / Walker, D.
History
DepositionNov 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized lipoprotein YfhM


Theoretical massNumber of molelcules
Total (without water)181,6181
Polymers181,6181
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)176.065, 176.065, 161.131
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Uncharacterized lipoprotein YfhM


Mass: 181618.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2520, JW2504, yfhM / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76578

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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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M potassium chloride, 25% SOKALAN CP7, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.65→46.87 Å / Num. all: 20753 / Num. obs: 20753 / % possible obs: 99.9 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 26.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.2
Reflection shellResolution: 3.65→4 Å / Redundancy: 26.7 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
EDNAdata collection
AutoSolphasing
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.65→46.87 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 76.202 / SU ML: 0.491 / Cross valid method: THROUGHOUT / ESU R Free: 0.588 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23831 1033 5 %RANDOM
Rwork0.17746 ---
all0.18042 20753 --
obs0.18042 19679 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 144.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 3.65→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8699 0 0 0 8699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198882
X-RAY DIFFRACTIONr_bond_other_d0.0020.028449
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.97512081
X-RAY DIFFRACTIONr_angle_other_deg0.834319429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47551117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8524.903414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.308151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8811557
X-RAY DIFFRACTIONr_chiral_restr0.0750.21340
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110228
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021991
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.5111.2914483
X-RAY DIFFRACTIONr_mcbond_other6.50811.2924482
X-RAY DIFFRACTIONr_mcangle_it10.55216.9275595
X-RAY DIFFRACTIONr_mcangle_other10.55116.9275596
X-RAY DIFFRACTIONr_scbond_it6.23711.7554399
X-RAY DIFFRACTIONr_scbond_other6.23611.7544400
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.1917.4626487
X-RAY DIFFRACTIONr_long_range_B_refined15.88992.52210186
X-RAY DIFFRACTIONr_long_range_B_other15.88892.52110187
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.65→3.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 73 -
Rwork0.311 1462 -
obs--99.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.80020.3070.20461.9879-0.22670.10270.0268-0.3910.04340.2979-0.1047-0.33150.0508-0.08650.07790.2358-0.03080.02040.3827-0.0210.087-46.647334.2593-18.8426
24.4261-1.8128-1.15692.56140.88581.0922-0.0577-0.3034-0.5074-0.00460.2075-0.0550.23630.3302-0.14980.46360.0111-0.03390.34190.09230.2591-45.2246-3.2228-28.3827
31.83050.1571-0.46831.7705-0.77930.89880.05670.0402-0.1042-0.2949-0.07420.24550.1612-0.17030.01750.1727-0.0620.01070.1372-0.07350.0813-66.865129.179-41.9534
42.5169-1.5513-0.69281.4903-0.06953.87920.00260.0873-0.23790.1323-0.11470.46910.144-0.30590.1120.0826-0.05630.07830.0617-0.03120.3837-34.930735.1078-83.4727
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A379 - 485
2X-RAY DIFFRACTION1A853 - 922
3X-RAY DIFFRACTION1A943 - 1019
4X-RAY DIFFRACTION2A486 - 610
5X-RAY DIFFRACTION2A611 - 622
6X-RAY DIFFRACTION2A637 - 677
7X-RAY DIFFRACTION2A691 - 743
8X-RAY DIFFRACTION3A1020 - 1127
9X-RAY DIFFRACTION3A1128 - 1168
10X-RAY DIFFRACTION3A1440 - 1498
11X-RAY DIFFRACTION3A1499 - 1560
12X-RAY DIFFRACTION3A1566 - 1653
13X-RAY DIFFRACTION4A1169 - 1439

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