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- PDB-7dpy: Structure of Brucella abortus PhiA -

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Basic information

Entry
Database: PDB / ID: 7dpy
TitleStructure of Brucella abortus PhiA
ComponentsBrucella Abortus PhiA
KeywordsUNKNOWN FUNCTION / T4SS / lysozyme inhibitor / PliC
Function / homologyC-type lysozyme inhibitor superfamily / C-type lysozyme inhibitor / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta / C-type lysozyme inhibitor domain-containing protein
Function and homology information
Biological speciesBrucella abortus bv. 1 str. 9-941 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHyun, Y. / Ha, N.-C.
CitationJournal: Mol.Cells / Year: 2021
Title: Structure and Function of the Autolysin SagA in the Type IV Secretion System of Brucella abortus .
Authors: Hyun, Y. / Baek, Y. / Lee, C. / Ki, N. / Ahn, J. / Ryu, S. / Ha, N.C.
History
DepositionDec 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 13, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Brucella Abortus PhiA
B: Brucella Abortus PhiA


Theoretical massNumber of molelcules
Total (without water)24,5352
Polymers24,5352
Non-polymers00
Water2,126118
1
A: Brucella Abortus PhiA
B: Brucella Abortus PhiA

A: Brucella Abortus PhiA
B: Brucella Abortus PhiA


Theoretical massNumber of molelcules
Total (without water)49,0704
Polymers49,0704
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5120 Å2
ΔGint-32 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.155, 51.156, 62.303
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLUGLU(chain 'A' and (resid 68 through 141 or resid 147 through 157))AA68 - 1408 - 80
12GLUGLUASPASP(chain 'A' and (resid 68 through 141 or resid 147 through 157))AA147 - 15787 - 97
23PROPROGLUGLU(chain 'B' and resid 68 through 157)BB68 - 1408 - 80
24GLUGLUASPASP(chain 'B' and resid 68 through 157)BB147 - 15787 - 97

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Components

#1: Protein Brucella Abortus PhiA


Mass: 12267.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal sequence was confirmed by Edman degradation sequencing method. 101-108 residues are expression tag sequence, for both chain A and B.
Source: (gene. exp.) Brucella abortus bv. 1 str. 9-941 (bacteria)
Strain: 9-941 / Gene: BruAb1_0102 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57FR6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M BIS-TRIS pH 6.0, 18% (w/v) PEG 10000

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 19949 / % possible obs: 99 % / Redundancy: 9.7 % / Biso Wilson estimate: 17.16 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.025 / Rrim(I) all: 0.086 / Net I/σ(I): 23.7
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.311 / Num. unique obs: 964 / CC1/2: 0.953 / CC star: 0.988 / Rpim(I) all: 0.097 / Rrim(I) all: 0.276

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MIR

4mir


Resolution: 1.8→45.36 Å / SU ML: 0.1729 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 21.487
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2309 1033 5.21 %
Rwork0.1992 18804 -
obs0.2009 19837 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.73 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 0 118 1511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071418
X-RAY DIFFRACTIONf_angle_d0.95091926
X-RAY DIFFRACTIONf_chiral_restr0.0665218
X-RAY DIFFRACTIONf_plane_restr0.0054249
X-RAY DIFFRACTIONf_dihedral_angle_d23.5502517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.90.24391440.20322521X-RAY DIFFRACTION93.57
1.9-2.020.24211680.18922595X-RAY DIFFRACTION98.47
2.02-2.170.26681200.19772698X-RAY DIFFRACTION99.02
2.17-2.390.25221480.20882674X-RAY DIFFRACTION99.19
2.39-2.740.27171260.21722709X-RAY DIFFRACTION99.44
2.74-3.450.25411430.2022755X-RAY DIFFRACTION99.66
3.45-45.360.18991840.18882852X-RAY DIFFRACTION99.74

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