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- PDB-3gxa: Crystal structure of GNA1946 -

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Basic information

Entry
Database: PDB / ID: 3gxa
TitleCrystal structure of GNA1946
ComponentsOuter membrane lipoprotein GNA1946
KeywordsPROTEIN BINDING / PERIPLASMIC / LIPOPROTEIN / L-METHIONINE BINGDING
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
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsYang, X. / Shen, Y.
CitationJournal: J.Struct.Biol. / Year: 2009
Title: Crystal structure of lipoprotein GNA1946 from Neisseria meningitidis
Authors: Yang, X. / Wu, Z. / Wang, X. / Yang, C. / Xu, H. / Shen, Y.
History
DepositionApr 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane lipoprotein GNA1946
B: Outer membrane lipoprotein GNA1946
C: Outer membrane lipoprotein GNA1946
D: Outer membrane lipoprotein GNA1946
E: Outer membrane lipoprotein GNA1946
F: Outer membrane lipoprotein GNA1946
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,59328
Polymers182,1606
Non-polymers2,43222
Water12,232679
1
A: Outer membrane lipoprotein GNA1946
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7014
Polymers30,3601
Non-polymers3413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer membrane lipoprotein GNA1946
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0868
Polymers30,3601
Non-polymers7267
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Outer membrane lipoprotein GNA1946
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6053
Polymers30,3601
Non-polymers2452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Outer membrane lipoprotein GNA1946
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8946
Polymers30,3601
Non-polymers5335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Outer membrane lipoprotein GNA1946
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6053
Polymers30,3601
Non-polymers2452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Outer membrane lipoprotein GNA1946
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7014
Polymers30,3601
Non-polymers3413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.395, 122.809, 160.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Outer membrane lipoprotein GNA1946


Mass: 30360.082 Da / Num. of mol.: 6 / Fragment: residues in UNP 22-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: gna1946 / Plasmid: pET-21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7BMQ8
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 679 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1M Citrc Acid, 2M ammonium sulfate, 0.5% N-Dodecyl-beta-D-Maltoside, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.5415
SYNCHROTRONBSRF 3W1A20.9791
ROTATING ANODERIGAKU MICROMAX-007 HF31.5415
Detector
TypeIDDetectorDate
RIGAKU RAXIS HTC1IMAGE PLATENov 2, 2008
MAR CCD 165 mm2CCDDec 30, 2008
RIGAKU RAXIS HTC3IMAGE PLATEMar 1, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54151
20.97911
ReflectionResolution: 2.25→50 Å / Num. all: 101618 / Num. obs: 96412 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.5 / Redundancy: 4.6 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.098 / Net I/σ(I): 2.1
Reflection shellResolution: 2.25→2.35 Å / % possible all: 94.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.25→21.55 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 96391.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.239 4872 5.1 %RANDOM
Rwork0.206 ---
obs0.206 96412 94.4 %-
all-101618 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.393 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.4 Å20 Å20 Å2
2---6.14 Å20 Å2
3----2.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.25→21.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11366 0 134 679 12179
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 722 4.9 %
Rwork0.266 14015 -
obs--87.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3so4.paramso4.top
X-RAY DIFFRACTION4met.parammet.top

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