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- PDB-4mis: The structure of Brucella abortus PliC in the orthorombic crystal form -

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Basic information

Entry
Database: PDB / ID: 4mis
TitleThe structure of Brucella abortus PliC in the orthorombic 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 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 1.1Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)21,2942
Polymers21,2942
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-23 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.283, 64.448, 47.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein


Mass: 10646.972 Da / Num. of mol.: 2 / 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.: 111 / 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: 3.29 Å3/Da / Density % sol: 62.56 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.9M ammonium sulfate, 0.1M Tris-HCl, 10% glycerol, pH 8.5, 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: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2012
RadiationMonochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 19081 / Num. obs: 18850 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2-2.03187.7
2.03-2.07188
2.07-2.11190.9
2.11-2.15191.1

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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→19.601 Å / SU ML: 0.26 / σ(F): 1.57 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 976 5.18 %RANDOM
Rwork0.2147 ---
obs0.2171 18311 96.32 %-
all-19570 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1479 0 0 111 1590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081514
X-RAY DIFFRACTIONf_angle_d1.0932055
X-RAY DIFFRACTIONf_dihedral_angle_d14.658547
X-RAY DIFFRACTIONf_chiral_restr0.07243
X-RAY DIFFRACTIONf_plane_restr0.004255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.10540.29221250.2786232089
2.1054-2.23710.33211370.2628245194
2.2371-2.40950.31921360.2418251997
2.4095-2.65150.28391540.2272254897
2.6515-3.0340.26021650.2123257298
3.034-3.81780.24451250.1879267799
3.8178-19.60170.22751340.1961278799

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