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- PDB-4ml7: Crystal structure of Brucella abortus PliC in complex with human ... -

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Basic information

Entry
Database: PDB / ID: 4ml7
TitleCrystal structure of Brucella abortus PliC in complex with human lysozyme
Components
  • Humanlysozyme
  • Lysozyme C
KeywordsHYDROLASE / inhibitor / lysozyme
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
C-type lysozyme inhibitor / Lysozyme - #10 / Lipocalin / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C ...C-type lysozyme inhibitor / Lysozyme - #10 / Lipocalin / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
B: Humanlysozyme
C: Lysozyme C
D: Humanlysozyme


Theoretical massNumber of molelcules
Total (without water)50,7354
Polymers50,7354
Non-polymers00
Water8,215456
1
A: Lysozyme C
B: Humanlysozyme


Theoretical massNumber of molelcules
Total (without water)25,3682
Polymers25,3682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint1 kcal/mol
Surface area11340 Å2
MethodPISA
2
C: Lysozyme C
D: Humanlysozyme


Theoretical massNumber of molelcules
Total (without water)25,3682
Polymers25,3682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint1 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.253, 88.984, 66.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C


Mass: 14720.693 Da / Num. of mol.: 2 / Fragment: UNP residues 19-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYZ, LZM / Production host: Escherichia coli (E. coli) / References: UniProt: P61626, lysozyme
#2: Protein Humanlysozyme


Mass: 10646.972 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Oryza sativa (Asian cultivated rice)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THE CHAIN B AND D DOES NOT CURRENTLY EXIST.

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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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate tribasic, 40% tert-butanol, pH 5.6, 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: 0.9795 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: 1.8→20 Å / Num. all: 53944 / Num. obs: 53896 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.8-1.83199.8
1.83-1.86199.9
1.86-1.9197.1
1.9-1.94188.4
1.94-1.98199.1
1.98-2.03199.9
2.03-2.08197.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.982 Å / SU ML: 0.18 / σ(F): 1.53 / Phase error: 19.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 2725 5.06 %RNADOM
Rwork0.1855 ---
obs0.1873 52158 96.72 %-
all-55723 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→19.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3534 0 0 456 3990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073704
X-RAY DIFFRACTIONf_angle_d1.1095019
X-RAY DIFFRACTIONf_dihedral_angle_d12.6161352
X-RAY DIFFRACTIONf_chiral_restr0.079548
X-RAY DIFFRACTIONf_plane_restr0.004650
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.8310.22991450.1923266496
1.831-1.86620.26621370.22746100
1.8662-1.90430.2541340.2287256994
1.9043-1.94570.32711290.3116256892
1.9457-1.99090.24231750.19682689100
1.9909-2.04060.24321370.19232733100
2.0406-2.09570.26191430.1965270598
2.0957-2.15730.20511370.18282758100
2.1573-2.22690.23011540.1791271698
2.2269-2.30640.26131290.2097247590
2.3064-2.39860.22041340.17852765100
2.3986-2.50750.21161610.1822759100
2.5075-2.63950.19951480.18372783100
2.6395-2.80440.21191630.17552743100
2.8044-3.02030.24191350.1816280099
3.0203-3.3230.18941580.1756278599
3.323-3.80090.23631200.1768255590
3.8009-4.77790.18821340.1596250988
4.7779-19.98320.20581520.1789284996

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