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- PDB-4yu5: Crystal structure of selenomethionine variant of Bacillus anthrac... -

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Basic information

Entry
Database: PDB / ID: 4yu5
TitleCrystal structure of selenomethionine variant of Bacillus anthracis immune inhibitor A2 peptidase zymogen
ComponentsImmune inhibitor A, metalloprotease
KeywordsHYDROLASE / metallopeptidase / metzincin
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metallopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M6, InhA / Peptidase M6-like, domain / Immune inhibitor A peptidase M6, catalytic domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / 3-(1-methylpiperidinium-1-yl)propane-1-sulfonate / Immune inhibitor A, metalloprotease
Similarity search - Component
Biological speciesBacillus cereus var. anthracis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsArolas, J.L. / Goulas, T. / Gomis-Ruth, F.X.
CitationJournal: Structure / Year: 2016
Title: Structural Basis for Latency and Function of Immune Inhibitor A Metallopeptidase, a Modulator of the Bacillus anthracis Secretome.
Authors: Arolas, J.L. / Goulas, T. / Pomerantsev, A.P. / Leppla, S.H. / Gomis-Ruth, F.X.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immune inhibitor A, metalloprotease
B: Immune inhibitor A, metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,73521
Polymers168,2492
Non-polymers1,48619
Water1,874104
1
A: Immune inhibitor A, metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,34514
Polymers84,1251
Non-polymers1,22113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immune inhibitor A, metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3897
Polymers84,1251
Non-polymers2656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.610, 102.410, 242.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Immune inhibitor A, metalloprotease


Mass: 84124.500 Da / Num. of mol.: 2 / Fragment: residues 50-799 / Mutation: E331A
Source method: isolated from a genetically manipulated source
Details: The conflicts are due to the uniprot entry being for a different strain
Source: (gene. exp.) Bacillus cereus var. anthracis (strain CI) (bacteria)
Strain: CI / Gene: inhA2, BACI_c06810 / Plasmid: pHT43 / Production host: Bacillus subtilis (bacteria) / Strain (production host): WB800N
References: UniProt: D8H130, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 6 types, 123 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-KH2 / 3-(1-methylpiperidinium-1-yl)propane-1-sulfonate


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M BIS-TRIS propane, 0.2 M potassium sodium tartrate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926, 0.93923
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2014
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.939231
ReflectionResolution: 2.9→48.8 Å / Num. obs: 54813 / % possible obs: 99.8 % / Redundancy: 8.4 % / Biso Wilson estimate: 74.38 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 15.2
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 4.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
Cootmodel building
SHELXphasing
BUSTER2.11.5refinement
RefinementMethod to determine structure: MAD / Resolution: 2.9→42.46 Å / Cor.coef. Fo:Fc: 0.9105 / Cor.coef. Fo:Fc free: 0.9075 / SU R Cruickshank DPI: 0.529 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.5 / SU Rfree Blow DPI: 0.261 / SU Rfree Cruickshank DPI: 0.268
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 706 1.29 %RANDOM
Rwork0.1824 ---
obs0.1827 54706 99.86 %-
Displacement parametersBiso mean: 71.82 Å2
Baniso -1Baniso -2Baniso -3
1-6.4017 Å20 Å20 Å2
2---25.8688 Å20 Å2
3---19.467 Å2
Refine analyzeLuzzati coordinate error obs: 0.438 Å
Refinement stepCycle: 1 / Resolution: 2.9→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10763 0 75 104 10942
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111078HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1414973HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5007SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes311HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1599HARMONIC5
X-RAY DIFFRACTIONt_it11078HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion3.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1362SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12043SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3637 50 1.26 %
Rwork0.2415 3917 -
all0.2429 3967 -
obs--99.86 %
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)
11.2482-0.12640.18541.50040.99762.62750.13580.2892-0.1899-0.11560.0933-0.0757-0.12650.0254-0.2291-0.1532-0.01880.0005-0.0884-0.05-0.122483.879442.1481249.355
23.4851.6277-2.00692.7758-2.11418.1155-0.0064-0.03-0.27090.17230.15010.3590.6357-0.5908-0.14370.19-0.12930.1385-0.11840.01690.035196.241973.9219221.201
34.85960.82322.249901.62694.6003-0.05450.24730.21840.02760.3758-0.2405-0.06270.2392-0.3213-0.13910.0714-0.08020.1245-0.26710.3759103.21932.4421245.098
41.39050.12860.33241.6845-0.07273.0222-0.1433-0.4216-0.20030.64490.2387-0.23460.3695-0.0775-0.09540.34580.2033-0.0544-0.08810.0107-0.09986.255324.1315181.177
54.39510.6725-3.19212.3609-0.17246.0220.06490.16230.386-0.29340.1797-0.3163-0.37080.3622-0.24460.1723-0.11790.0755-0.06070.0453-0.021647.266914.1304199.106
60-1.532-0.42865.9498-1.6347.0394-0.015-0.0428-0.2158-0.0262-0.0272-0.1290.11270.01340.04220.58240.2749-0.117-0.0815-0.00330.335697.22153.3767181.354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|144 - 482 A|642 - 799 A|901 - 903 A|995 - 999}
2X-RAY DIFFRACTION2{A|483 - 641}
3X-RAY DIFFRACTION3{A|50 - 94}
4X-RAY DIFFRACTION4{B|144 - 482 B|642 - 799 B|901 - 902 B|995 - 999}
5X-RAY DIFFRACTION5{B|483 - 641}
6X-RAY DIFFRACTION6{B|50 - 89}

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