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- PDB-3bf2: Crystal structure of the A1KSW9_NEIMF protein from Neisseria meni... -

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Basic information

Entry
Database: PDB / ID: 3bf2
TitleCrystal structure of the A1KSW9_NEIMF protein from Neisseria meningitidis. Northeast Structural Genomics Consortium target MR36a
ComponentsPutative lipoprotein
KeywordsLIPOPROTEIN / NESG / MR36a / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


transporter complex / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane
Similarity search - Function
Lipoprotein like domain / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Double Stranded RNA Binding Domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
LPS-assembly lipoprotein LptE
Similarity search - Component
Biological speciesNeisseria meningitidis FAM18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsVorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Cunningham, K. / Maglaqui, M. / Owens, L. / Fang, Y. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Cunningham, K. / Maglaqui, M. / Owens, L. / Fang, Y. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the A1KSW9_NEIMF protein from Neisseria meningitidis.
Authors: Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Cunningham, K. / Maglaqui, M. / Owens, L. / Fang, Y. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionNov 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)17,3321
Polymers17,3321
Non-polymers00
Water68538
1
A: Putative lipoprotein

A: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)34,6642
Polymers34,6642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z+1/21
Unit cell
Length a, b, c (Å)65.296, 65.296, 92.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
DetailsDimer according to analytical gel filtration

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Components

#1: Protein Putative lipoprotein


Mass: 17331.871 Da / Num. of mol.: 1 / Fragment: Residues 17-159 / Mutation: L20M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis FAM18 (bacteria)
Species: Neisseria meningitidis / Strain: FAM18 / Serogroup C / Serotype 2a / Gene: NMC0657 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: A1KSW9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.5 M Li chloride, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97910, 0.97940, 0.96785
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.967851
ReflectionResolution: 2.6→50 Å / Num. all: 11698 / Num. obs: 11698 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.1 % / Biso Wilson estimate: 54.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 36.89
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 15.5 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 6.72 / Num. unique all: 1286 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→41.31 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 563251.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.258 552 5 %RANDOM
Rwork0.226 ---
obs0.226 10968 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.3514 Å2 / ksol: 0.34641 e/Å3
Displacement parametersBiso mean: 57.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.85 Å20 Å20 Å2
2--4.85 Å20 Å2
3----9.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.6→41.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 0 38 982
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 100 6.3 %
Rwork0.275 1493 -
obs--80.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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