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- PDB-6eup: Crystal structure of Neisseria meningitidis NadA variant 3 double... -

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Basic information

Entry
Database: PDB / ID: 6eup
TitleCrystal structure of Neisseria meningitidis NadA variant 3 double mutant A33I-I38L
ComponentsAdhesin A
KeywordsCELL ADHESION / trimeric autotransporter adhesin / antigen / double mutant
Function / homologyTrimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / cell surface / membrane / PHOSPHATE ION / Adhesin A
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 31, 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 A
B: Adhesin A
C: Adhesin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,86232
Polymers50,2693
Non-polymers2,59329
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18750 Å2
ΔGint-166 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.919, 39.750, 255.630
Angle α, β, γ (deg.)90.00, 95.13, 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 A / NadA autotransporter / Putative adhesin/invasin


Mass: 16756.418 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: nadA, nadA_1, ERS040961_00445 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KH85

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Non-polymers , 6 types, 82 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.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.47 Å3/Da / Density % sol: 64.54 %
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: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.65→63.65 Å / Num. obs: 18251 / % possible obs: 89.1 % / Redundancy: 2.7 % / Biso Wilson estimate: 35.35 Å2 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.098 / Net I/σ(I): 8
Reflection shellResolution: 2.65→2.79 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2415 / Rrim(I) all: 0.494 / % possible all: 84.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→63.65 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.499 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.486 / SU Rfree Blow DPI: 0.279 / SU Rfree Cruickshank DPI: 0.285
RfactorNum. reflection% reflectionSelection details
Rfree0.236 995 5.45 %RANDOM
Rwork0.198 ---
obs0.2 18248 88.9 %-
Displacement parametersBiso mean: 65.93 Å2
Baniso -1Baniso -2Baniso -3
1--9.6667 Å20 Å2-3.9169 Å2
2---9.5471 Å20 Å2
3---19.2138 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.65→63.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 166 53 3513
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013446HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.144611HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1256SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes126HARMONIC2
X-RAY DIFFRACTIONt_gen_planes456HARMONIC5
X-RAY DIFFRACTIONt_it3446HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.05
X-RAY DIFFRACTIONt_other_torsion20.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion506SEMIHARMONIC5
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_contact3855SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.262 140 5.21 %
Rwork0.217 2549 -
all0.219 2689 -
obs--84.23 %
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)
10.15760.0669-1.4420.004-0.444912.57180.0348-0.17440.05110.09760.03270.02790.4957-0.0267-0.0675-0.0606-0.0651-0.01090.0724-0.006-0.09098.8481-1.214560.3887
20.1475-0.03320.94080.0746-0.627210.913-0.0024-0.1396-0.06180.15330.00860.013-0.18590.4803-0.0062-0.11240.0578-0.0420.07150.0049-0.08313.6814-2.09460.3863
30.03470.00580.37370.13251.276813.73120.033-0.17710.00050.1166-0.0213-0.0896-0.3861-0.4733-0.01180.00550.0056-0.0304-0.0401-0.0105-0.094112.02172.531160.405
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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