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- PDB-6eun: Crystal structure of Neisseria meningitidis vaccine antigen NadA ... -

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Basic information

Entry
Database: PDB / ID: 6eun
TitleCrystal structure of Neisseria meningitidis vaccine antigen NadA variant 3
ComponentsAdhesin
KeywordsCELL ADHESION / trimeric autotransporter adhesin / antigen
Function / homology
Function and homology information


cell surface / membrane
Similarity search - Function
Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like
Similarity search - Domain/homology
CITRIC ACID / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Adhesin A / Adhesin A
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDello Iacono, L. / Liguori, A. / Malito, E. / Bottomley, M.J.
CitationJournal: MBio / Year: 2018
Title: NadA3 Structures Reveal Undecad Coiled Coils and LOX1 Binding Regions Competed by Meningococcus B Vaccine-Elicited Human Antibodies.
Authors: Liguori, A. / Dello Iacono, L. / Maruggi, G. / Benucci, B. / Merola, M. / Lo Surdo, P. / Lopez-Sagaseta, J. / Pizza, M. / Malito, E. / Bottomley, M.J.
History
DepositionOct 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Adhesin
C: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,85130
Polymers50,1433
Non-polymers2,70827
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18190 Å2
ΔGint-121 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.761, 39.778, 255.494
Angle α, β, γ (deg.)90.00, 95.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Adhesin / Adhesin A / NadA


Mass: 16714.338 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: nadA, A6L27_04700 / Production host: Escherichia coli (E. coli) / References: UniProt: A0ELI3, UniProt: Q8KH85*PLUS

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Non-polymers , 9 types, 79 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#7: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium phosphate citrate pH 3.9, 5% (w/v) PEG 1K, 33.6-45.9% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.45→34.84 Å / Num. obs: 23543 / % possible obs: 91.3 % / Redundancy: 2.5 % / Biso Wilson estimate: 55.36 Å2 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.062 / Net I/σ(I): 9.5
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3487 / Rrim(I) all: 0.474 / % possible all: 94.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→34.84 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.303 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.297 / SU Rfree Blow DPI: 0.214 / SU Rfree Cruickshank DPI: 0.219
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1141 4.85 %RANDOM
Rwork0.199 ---
obs0.2 23542 89.4 %-
Displacement parametersBiso mean: 88.66 Å2
Baniso -1Baniso -2Baniso -3
1--12.6741 Å20 Å20.1189 Å2
2---9.6965 Å20 Å2
3---22.3706 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.45→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3247 0 173 52 3472
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013406HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.144555HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1242SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes126HARMONIC2
X-RAY DIFFRACTIONt_gen_planes453HARMONIC5
X-RAY DIFFRACTIONt_it3406HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.14
X-RAY DIFFRACTIONt_other_torsion21.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion497SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3771SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.253 112 4.01 %
Rwork0.231 2684 -
all0.232 2796 -
obs--87.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.125-0.09010.70810.0671-0.873211.35770.0176-0.1209-0.05710.13850.04340.0374-0.23170.2956-0.061-0.06820.0051-0.0035-0.03260.00840.001713.8438-1.845160.3375
20.02330.01170.38080.18540.99211.63410.0567-0.12920.01220.1420.0209-0.0526-0.1811-0.3022-0.0776-0.011-0.00030.0152-0.0602-0.013-0.004512.00562.966861.9614
30.13070.0738-1.23810-0.341911.46890.0445-0.15840.05720.1190.04430.04230.3276-0.0145-0.08870.0213-0.04540.02210.01110.0133-0.03688.8509-1.125561.9758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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