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- PDB-7wzb: lipopolysaccharide assembly protein LapB (open) -

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Basic information

Entry
Database: PDB / ID: 7wzb
Titlelipopolysaccharide assembly protein LapB (open)
ComponentsLipopolysaccharide assembly protein B
KeywordsMEMBRANE PROTEIN / lipopolysaccharide assembly protein LapB (open) cytoplasmic soluble domain
Function / homology
Function and homology information


lipopolysaccharide metabolic process / regulation of lipid biosynthetic process / transferase activity / iron ion binding / cell division / plasma membrane
Similarity search - Function
Lipopolysaccharide assembly protein B / LapB, rubredoxin metal binding domain / Rubredoxin metal binding domain / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Lipopolysaccharide assembly protein B
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYan, L. / Dong, H. / Li, H. / Liu, X. / Deng, Z. / Dong, C. / Zhang, Z.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0903200 China
Ministry of Science and Technology (MoST, China)2021YFC2100600 China
National Natural Science Foundation of China (NSFC)31800052 China
CitationJournal: To Be Published
Title: lipopolysaccharide assembly protein LapB (open)
Authors: Yan, L. / Dong, H. / Li, H. / Liu, X. / Deng, Z. / Dong, C. / Zhang, Z.
History
DepositionFeb 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Lipopolysaccharide assembly protein B
A: Lipopolysaccharide assembly protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0485
Polymers84,7672
Non-polymers2813
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-15 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.080, 78.960, 124.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Lipopolysaccharide assembly protein B


Mass: 42383.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: lipopolysaccharide assembly protein B
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / Gene: lapB / Plasmid: pet28 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7CQG6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8 / Details: 21.25% Ethylene glycol 15% glycerol / PH range: 7-8

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9175 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9175 Å / Relative weight: 1
ReflectionResolution: 2.7→24.72 Å / Num. obs: 19835 / % possible obs: 97.03 % / Redundancy: 7.3 % / Biso Wilson estimate: 41.78 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04174 / Rpim(I) all: 0.01674 / Rrim(I) all: 0.04506 / Net I/σ(I): 27.93
Reflection shellResolution: 2.7→2.796 Å / Redundancy: 7.08 % / Rmerge(I) obs: 0.2306 / Mean I/σ(I) obs: 7.08 / Num. unique obs: 1537 / CC1/2: 0.991 / CC star: 0.998 / Rpim(I) all: 0.08943 / Rrim(I) all: 0.2476 / % possible all: 78.14

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZLH

4zlh


Resolution: 2.7→24.46 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 979 4.73 %
Rwork0.248 18896 -
obs-19490 97.03 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.98 Å2 / Biso mean: 73.9629 Å2 / Biso min: 37.84 Å2
Refinement stepCycle: final / Resolution: 2.7→24.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 12 17 3885
Biso mean--68.82 61 -
Num. residues----505
LS refinement shellResolution: 2.7→2.796 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3431 86 -
Rwork0.3407 979 -
obs--78.14 %
Refinement TLS params.Method: refined / Origin x: 13.8983 Å / Origin y: -17.2672 Å / Origin z: -9.0542 Å
111213212223313233
T0.4618 Å20.0226 Å20.0149 Å2-0.4729 Å2-0.0085 Å2--0.4731 Å2
L0.7916 °20.9271 °2-0.1231 °2-0.478 °20.0529 °2--0.3516 °2
S0.0301 Å °-0.1372 Å °-0.0356 Å °-0.1046 Å °-0.0203 Å °0.0151 Å °-0.0285 Å °0.0682 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB135 - 400
2X-RAY DIFFRACTION1allA137 - 400
3X-RAY DIFFRACTION1allX500
4X-RAY DIFFRACTION1allS1 - 18

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