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- PDB-4mir: The structure of Brucella abortus PliC in the hexagonal crystal form -

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Basic information

Entry
Database: PDB / ID: 4mir
TitleThe structure of Brucella abortus PliC in the hexagonal crystal form
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE INHIBITOR / lysozyme
Function / homologyC-type lysozyme inhibitor / Membrane-bound lysozyme-inhibitor of c-type lysozyme / C-type lysozyme inhibitor superfamily / C-type lysozyme inhibitor / Lipocalin / Beta Barrel / Mainly Beta / membrane / C-type lysozyme inhibitor domain-containing protein
Function and homology information
Biological speciesBrucella abortus bv. 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHa, N.C. / Um, S.H. / Kim, J.S.
CitationJournal: Biochemistry / Year: 2013
Title: Structural basis for the inhibition of human lysozyme by PliC from Brucella abortus
Authors: Um, S.H. / Kim, J.S. / Kim, K. / Kim, N. / Cho, H.S. / Ha, N.C.
History
DepositionSep 2, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)31,9413
Polymers31,9413
Non-polymers00
Water2,360131
1
A: Putative uncharacterized protein

A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)21,2942
Polymers21,2942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area3120 Å2
ΔGint-23 kcal/mol
Surface area10120 Å2
MethodPISA
2
B: Putative uncharacterized protein
C: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)21,2942
Polymers21,2942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-22 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.395, 58.395, 364.763
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-253-

HOH

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Components

#1: Protein Putative uncharacterized protein


Mass: 10646.972 Da / Num. of mol.: 3 / Fragment: UNP residues 27-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus bv. 1 (bacteria) / Strain: 9-941 / Gene: BruAb1_0462 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57ES7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 2.0M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 287.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 5, 2012
RadiationMonochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 15664 / Num. obs: 15422 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.4-2.44197.5
2.44-2.49198
2.49-2.53198.7
2.53-2.58198.6
2.58-2.64198.2
2.64-2.7198.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.752 Å / SU ML: 0.35 / σ(F): 1.52 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2703 764 4.96 %RANDOM
Rwork0.2072 ---
obs0.2103 15406 99.04 %-
all-15555 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→19.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 0 131 2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082242
X-RAY DIFFRACTIONf_angle_d1.1553041
X-RAY DIFFRACTIONf_dihedral_angle_d15.226809
X-RAY DIFFRACTIONf_chiral_restr0.073359
X-RAY DIFFRACTIONf_plane_restr0.005377
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.5850.33871420.2566280999
2.585-2.84440.29261640.2396280799
2.8444-3.25440.31661550.224289099
3.2544-4.09420.25631560.1915291999
4.0942-19.7530.2311470.1883217100

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