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- PDB-4hrv: Crystal Structure of Lipoprotein GNA1162 from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 4hrv
TitleCrystal Structure of Lipoprotein GNA1162 from Neisseria meningitidis
ComponentsPutative lipoprotein GNA1162
KeywordsLIPID BINDING PROTEIN / DUF799
Function / homologyPutative lipoprotein GNA1162-like / Putative lipoprotein GNA1162-like / ABC-type transport auxiliary lipoprotein component / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Genome-derived Neisseria antigen 1162
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å
AuthorsLin, Z. / Cai, X. / Shen, Y.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of Neisseria meningitidis lipoprotein GNA1162
Authors: Cai, X. / Lu, J. / Wu, Z. / Yang, C. / Xu, H. / Lin, Z. / Shen, Y.
History
DepositionOct 28, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative lipoprotein GNA1162
B: Putative lipoprotein GNA1162


Theoretical massNumber of molelcules
Total (without water)36,2952
Polymers36,2952
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-41 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.912, 96.130, 44.977
Angle α, β, γ (deg.)90.00, 112.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative lipoprotein GNA1162


Mass: 18147.523 Da / Num. of mol.: 2 / Fragment: UNP residues 26-180 / Mutation: V56M, L86M, A166M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: gna1162 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7BMM3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% ethylene glycol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. all: 23423 / Num. obs: 22968 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.89→2.07 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.89→31.393 Å / SU ML: 0.25 / σ(F): 0.15 / Phase error: 28.26 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2502 2007 7.59 %
Rwork0.2316 --
obs0.233 22968 95.97 %
all-23423 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.023 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4728 Å2-0 Å28.9105 Å2
2---13.8538 Å2-0 Å2
3---10.3809 Å2
Refinement stepCycle: LAST / Resolution: 1.89→31.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 0 36 2124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062127
X-RAY DIFFRACTIONf_angle_d0.962904
X-RAY DIFFRACTIONf_dihedral_angle_d12.949745
X-RAY DIFFRACTIONf_chiral_restr0.061346
X-RAY DIFFRACTIONf_plane_restr0.004376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.89-1.95710.34291740.3179211383
1.9571-2.03540.29131850.2652234593
2.0354-2.1280.28952100.2527242796
2.128-2.24020.24952050.239246997
2.2402-2.38050.25791990.2338246297
2.3805-2.56420.25932060.2468248598
2.5642-2.82210.25562100.2387252899
2.8221-3.23010.31652010.2588253999
3.2301-4.06820.23162100.2252558100
4.0682-31.39710.21582070.2053250797
Refinement TLS params.Method: refined / Origin x: -2.1647 Å / Origin y: -13.0513 Å / Origin z: -13.6334 Å
111213212223313233
T0.3191 Å20.0041 Å20.0504 Å2-0.2793 Å2-0.0259 Å2--0.2014 Å2
L0.7321 °20.1396 °20.5521 °2-3.1145 °20.1241 °2---0.5477 °2
S0.09 Å °0.0415 Å °0.0536 Å °0.2107 Å °-0.083 Å °-0.14 Å °0.0133 Å °-0.0439 Å °0.0087 Å °
Refinement TLS groupSelection details: all

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