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- PDB-4yu6: Crystal structure of Bacillus anthracis immune inhibitor A2 pepti... -

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Basic information

Entry
Database: PDB / ID: 4yu6
TitleCrystal structure 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
ACETONITRILE / : / Immune inhibitor A, metalloprotease
Similarity search - Component
Biological speciesBacillus cereus var. anthracis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 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
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)168,05020
Polymers167,3112
Non-polymers73918
Water3,027168
1
A: Immune inhibitor A, metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,04711
Polymers83,6561
Non-polymers39210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immune inhibitor A, metalloprotease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0029
Polymers83,6561
Non-polymers3478
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.980, 108.870, 100.410
Angle α, β, γ (deg.)90.00, 119.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Immune inhibitor A, metalloprotease


Mass: 83655.539 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 annotation matching 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, 186 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.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3N
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
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: ESRF / Beamline: ID23-1 / Wavelength: 0.97934 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2014
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.6→47.7 Å / Num. obs: 51133 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 74.45 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 14.8
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 2.1 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
Cootmodel building
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→47.67 Å / Cor.coef. Fo:Fc: 0.9417 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.692 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.571 / SU Rfree Blow DPI: 0.252 / SU Rfree Cruickshank DPI: 0.261
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 729 1.43 %RANDOM
Rwork0.1708 ---
obs0.1714 51130 99.75 %-
Displacement parametersBiso mean: 61.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.8401 Å20 Å213.7073 Å2
2--2.8941 Å20 Å2
3----5.7342 Å2
Refine analyzeLuzzati coordinate error obs: 0.336 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11399 0 24 168 11591
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111676HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1515782HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5320SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes341HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1684HARMONIC5
X-RAY DIFFRACTIONt_it11676HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion2.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1443SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance65HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12413SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3566 44 1.18 %
Rwork0.2772 3681 -
all0.2782 3725 -
obs--99.75 %
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)
10.5869-0.20480.3121.8209-0.28730.6844-0.01660.17510.0384-0.1755-0.0489-0.060.01710.1820.0655-0.1125-0.0110.0199-0.0158-0.0198-0.06965.5521259.61130.8372
22.91931.04260.3813.6440.87480.9028-0.043-0.00160.10260.1039-0.150.1922-0.0445-0.13150.193-0.07280.0085-0.0045-0.0142-0.0631-0.0717-28.4772243.86625.0636
31.1012-0.1943-0.07751.9606-0.24090.6968-0.01970.21220.1364-0.2452-0.1262-0.0133-0.03590.10330.14590.21440.009-0.09560.28090.01840.17940.5755257.93825.3411
40.7944-0.57230.28262.7256-0.4560.93780.1132-0.1051-0.0533-0.0363-0.0610.05540.09550.0079-0.0522-0.1299-0.01090.0209-0.0623-0.0311-0.060758.3124259.69114.7327
51.8298-0.6440.2032.70650.39012.1777-0.0745-0.1906-0.1430.40750.03630.0588-0.03390.03350.0382-0.03150.05940.0179-0.03740.0131-0.075966.147240.408-22.5046
62.5415-0.7277-1.72783.8721-0.1750.7445-0.0398-0.02580.1096-0.02590.0063-0.1812-0.05280.11940.03350.042-0.0955-0.03130.0769-0.00630.309581.4274263.26520.0509
72.8814-1.8467-0.38721.1847-0.21092.62450.01180.01030.0328-0.0066-0.00630.0028-0.04780.0268-0.00550.27170.0422-0.02080.2227-0.0040.169935.0872283.1963.6926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|146 - 482 A|642 - 799 A|901 - 904}
2X-RAY DIFFRACTION2{A|483 - 641}
3X-RAY DIFFRACTION3{A|50 - 145}
4X-RAY DIFFRACTION4{B|146 - 482 B|642 - 799 B|901 - 902}
5X-RAY DIFFRACTION5{B|483 - 641}
6X-RAY DIFFRACTION6{B|50 - 88}
7X-RAY DIFFRACTION7{B|133 - 145}

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