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- PDB-3k2d: Crystal structure of Immunogenic lipoprotein A from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 3k2d
TitleCrystal structure of Immunogenic lipoprotein A from Vibrio vulnificus
ComponentsABC-type metal ion transport system, periplasmic component
KeywordsIMMUNE SYSTEM / alpha/beta domain
Function / homology
Function and homology information


Lipoprotein NlpA family / NlpA lipoprotein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHIONINE / Lipoprotein / Lipoprotein
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYu, S. / Rhee, S.
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of Toll-like receptor 2-activating lipoprotein IIpA from Vibrio vulnificus.
Authors: Yu, S. / Lee, N.Y. / Park, S.J. / Rhee, S.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC-type metal ion transport system, periplasmic component
B: ABC-type metal ion transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3894
Polymers52,0912
Non-polymers2982
Water2,810156
1
A: ABC-type metal ion transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1952
Polymers26,0451
Non-polymers1491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC-type metal ion transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1952
Polymers26,0451
Non-polymers1491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)273.600, 273.600, 273.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432

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Components

#1: Protein ABC-type metal ion transport system, periplasmic component / Immunogenic lipoprotein A / IlpA


Mass: 26045.436 Da / Num. of mol.: 2 / Fragment: UNP RESIDUED 29-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: ATCC 29307 / Gene: VV1_0294 / Plasmid: pET28a_TEV / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8DFC1, UniProt: A0A3Q0L1R9*PLUS
#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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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: 4.08 Å3/Da / Density % sol: 69.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M HEPES, 2.25M ammonium sulfate, 3% sorbitol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A11.23984
SYNCHROTRONPAL/PLS 6C121.23984
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJun 2, 2008
ADSC QUANTUM 2102CCDJul 15, 2008
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23984 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 25307 / Num. obs: 25307 / % possible obs: 100 % / Observed criterion σ(F): 2 / Redundancy: 82 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 38.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 77.6 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 15 / Num. unique all: 2702 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2535 9.2 %RANDOM
Rwork0.225 ---
all-25307 --
obs-22772 89.983 %-
Solvent computationBsol: 36.651 Å2
Displacement parametersBiso max: 63.85 Å2 / Biso mean: 30.8 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 0 18 156 3776
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0091.5
X-RAY DIFFRACTIONc_angle_d1.372
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 2.6→2.69 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2CNS_water_rep.param
X-RAY DIFFRACTION3fme.param

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