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- PDB-6gq4: Neisseria gonorrhoeae Adhesin Complex Protein -

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Basic information

Entry
Database: PDB / ID: 6gq4
TitleNeisseria gonorrhoeae Adhesin Complex Protein
ComponentsAdhesin
KeywordsIMMUNE SYSTEM / Neisseria gonorrhoeae-Adhesin Complex Protein / NGO1981 / bactericidal antibody / vaccine
Function / homology: / Adhesin
Function and homology information
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsOrr, C.M. / Tews, I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K027131/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/M027260/1 United Kingdom
CitationJournal: mSphere / Year: 2018
Title: Structure of the RecombinantNeisseria gonorrhoeaeAdhesin Complex Protein (rNg-ACP) and Generation of Murine Antibodies with Bactericidal Activity against Gonococci.
Authors: Almonacid-Mendoza, H.L. / Humbert, M.V. / Dijokaite, A. / Cleary, D.W. / Soo, Y. / Hung, M.C. / Orr, C.M. / Machelett, M.M. / Tews, I. / Christodoulides, M.
History
DepositionJun 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4162
Polymers12,3931
Non-polymers231
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area6570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.092, 30.936, 67.572
Angle α, β, γ (deg.)90.00, 103.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Adhesin


Mass: 12393.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: BZG33_11025, BZG34_11065 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A222R8P4, UniProt: A0A4T9UDA3*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Potassium Thionate, 30% W/V PEG2000 MME, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 1.65→32.88 Å / Num. obs: 12098 / % possible obs: 99.9 % / Redundancy: 7.6 % / Net I/σ(I): 14.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 6.4 / Num. unique obs: 593 / CC1/2: 0.987 / Rpim(I) all: 0.066 / Rrim(I) all: 0.182 / Χ2: 0.39 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→32.88 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.911 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17944 617 5.1 %RANDOM
Rwork0.12535 ---
obs0.12818 11478 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.048 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å20 Å20.33 Å2
2---4.52 Å20 Å2
3---1.81 Å2
Refinement stepCycle: 1 / Resolution: 1.65→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms800 0 1 145 946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.014870
X-RAY DIFFRACTIONr_bond_other_d0.0020.017798
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.671181
X-RAY DIFFRACTIONr_angle_other_deg1.0291.6541888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2865115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.9623.94738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72115163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.772153
X-RAY DIFFRACTIONr_chiral_restr0.1020.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02983
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02153
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4082.126439
X-RAY DIFFRACTIONr_mcbond_other3.3772.119438
X-RAY DIFFRACTIONr_mcangle_it4.43.203555
X-RAY DIFFRACTIONr_mcangle_other4.4073.21556
X-RAY DIFFRACTIONr_scbond_it5.3862.73431
X-RAY DIFFRACTIONr_scbond_other5.4282.745432
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6643.839625
X-RAY DIFFRACTIONr_long_range_B_refined9.48128.451970
X-RAY DIFFRACTIONr_long_range_B_other7.95826.869926
X-RAY DIFFRACTIONr_rigid_bond_restr13.76831668
X-RAY DIFFRACTIONr_sphericity_free46.97569
X-RAY DIFFRACTIONr_sphericity_bonded34.9251722
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 39 -
Rwork0.152 870 -
obs--99.89 %

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