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- PDB-5my7: Adhesin Complex Protein from Neisseria meningitidis -

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Basic information

Entry
Database: PDB / ID: 5my7
TitleAdhesin Complex Protein from Neisseria meningitidis
ComponentsAdhesin
KeywordsCELL ADHESION / lysozyme / Neisseria meningitidis / antigen
Function / homologyDI(HYDROXYETHYL)ETHER / Adhesin / Adhesin complex protein
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å
AuthorsDerrick, J.P. / Awanye, A.
CitationJournal: PLoS Pathog. / Year: 2017
Title: Structure of the Neisseria Adhesin Complex Protein (ACP) and its role as a novel lysozyme inhibitor.
Authors: Humbert, M.V. / Awanye, A.M. / Lian, L.Y. / Derrick, J.P. / Christodoulides, M.
History
DepositionJan 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 13, 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)13,5414
Polymers13,3051
Non-polymers2353
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-4 kcal/mol
Surface area5800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.470, 58.470, 51.561
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Adhesin


Mass: 13305.372 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence includes signal peptide / Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: N875_06250 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A8F5R9, UniProt: Q9JXD8*PLUS
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 32 / 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: 1.91 Å3/Da / Density % sol: 35.68 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25 mM Hepes/Na pH 7.5, 37 mM NaCl) with 200 nl precipitant solution containing 0.2 M lithium sulfate, 0.1 M sodium acetate pH 4.5 and 50 % w/v PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.4→50.64 Å / Num. obs: 20461 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.036 / Net I/σ(I): 13.5
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 6 % / Rmerge(I) obs: 0.997 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1001 / Rpim(I) all: 0.668 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0157refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.4→50.64 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.179 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.057 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20045 1023 5 %RANDOM
Rwork0.15979 ---
obs0.16191 19413 99.84 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.968 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.08 Å2-0 Å2
2---0.17 Å20 Å2
3---0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.4→50.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms714 0 15 32 761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02738
X-RAY DIFFRACTIONr_bond_other_d0.0040.02703
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.977986
X-RAY DIFFRACTIONr_angle_other_deg1.00331642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.109591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47725.51729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32815133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.218152
X-RAY DIFFRACTIONr_chiral_restr0.1040.2108
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02134
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_it2.142.444370
X-RAY DIFFRACTIONr_mcbond_other2.0622.442369
X-RAY DIFFRACTIONr_mcangle_it2.7263.669459
X-RAY DIFFRACTIONr_mcangle_other2.743.67460
X-RAY DIFFRACTIONr_scbond_it3.3572.992368
X-RAY DIFFRACTIONr_scbond_other3.3562.991368
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9094.232528
X-RAY DIFFRACTIONr_long_range_B_refined4.02328.22694
X-RAY DIFFRACTIONr_long_range_B_other4.0228.24695
X-RAY DIFFRACTIONr_rigid_bond_restr2.85531441
X-RAY DIFFRACTIONr_sphericity_free18.872526
X-RAY DIFFRACTIONr_sphericity_bonded11.84651438
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 73 -
Rwork0.28 1425 -
obs--99.87 %

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