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- PDB-4cjd: Crystal structure of Neisseria meningitidis trimeric autotranspor... -

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Basic information

Entry
Database: PDB / ID: 4cjd
TitleCrystal structure of Neisseria meningitidis trimeric autotransporter and vaccine antigen NadA
ComponentsNADA
KeywordsCELL ADHESION / TRIMERIC AUTO-TRANSPORTER (TAA) / COILED-COIL
Function / homologyTrimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / cell outer membrane / membrane => GO:0016020 / cell surface / IODIDE ION / NadA
Function and homology information
Biological speciesNEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.056 Å
AuthorsMalito, E. / Biancucci, M. / Spraggon, G. / Bottomley, M.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of the Meningococcal Vaccine Antigen Nada and Epitope Mapping of a Bactericidal Antibody.
Authors: Malito, E. / Biancucci, M. / Faleri, A. / Ferlenghi, I. / Scarselli, M. / Maruggi, G. / Lo Surdo, P. / Veggi, D. / Liguori, A. / Santini, L. / Bertoldi, I. / Petracca, R. / Marchi, S. / ...Authors: Malito, E. / Biancucci, M. / Faleri, A. / Ferlenghi, I. / Scarselli, M. / Maruggi, G. / Lo Surdo, P. / Veggi, D. / Liguori, A. / Santini, L. / Bertoldi, I. / Petracca, R. / Marchi, S. / Romagnoli, G. / Cartocci, E. / Vercellino, I. / Savino, S. / Spraggon, G. / Norais, N. / Pizza, M. / Rappuoli, R. / Masignani, V. / Bottomley, M.J.
History
DepositionDec 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: NADA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8585
Polymers22,3501
Non-polymers5084
Water1,802100
1
A: NADA
hetero molecules

A: NADA
hetero molecules

A: NADA
hetero molecules


  • defined by author&software
  • 68.6 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)68,57415
Polymers67,0513
Non-polymers1,52312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area7650 Å2
ΔGint-77.8 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.227, 51.227, 577.942
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1001-

IOD

21A-1002-

IOD

31A-1003-

IOD

41A-1004-

IOD

51A-2034-

HOH

61A-2077-

HOH

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Components

#1: Protein NADA / ADHESIN A


Mass: 22350.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Strain: M01-240320 / Variant: VARIANT 5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0ELI2
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE UNIPROT SEQUENCE PROVIDED HEREIN (A0ELI2) DOES NOT MATCH WITH THE SEQUENCE OF THE CLONE ...THE UNIPROT SEQUENCE PROVIDED HEREIN (A0ELI2) DOES NOT MATCH WITH THE SEQUENCE OF THE CLONE CRYSTALLISED, WHICH CORRESPONDS TO THE NATURAL VARIANT 5 OF NADA AND WHICH AT THE MOMENT LACKS A GENBANK OR UNIPROT ENTRY.

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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: 3.12 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 4 / Details: 10% TACSIMATE PH 4.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.54
DetectorType: PILATUS PILATUS 2M / Detector: PIXEL / Date: Aug 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→48.1 Å / Num. obs: 34971 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 34.8 Å2 / Rsym value: 0.06 / Net I/σ(I): 22.75
Reflection shellResolution: 2.06→2.18 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.18 / Rsym value: 0.82 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.056→48.162 Å / SU ML: 0.18 / σ(F): 3.5 / Phase error: 18.67 / Stereochemistry target values: ML
Details: RESIDUES 138-198 OF THE ORIGINAL CONSTRUCT WERE NOT MODELLED BECAUSE OF WEAK OR MISSING ELECTRON DENSITY, LIKELY DUE TO DISORDER.
RfactorNum. reflection% reflection
Rfree0.2071 1744 5 %
Rwork0.1818 --
obs0.183 34948 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42 Å2
Refinement stepCycle: LAST / Resolution: 2.056→48.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 4 100 1009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014912
X-RAY DIFFRACTIONf_angle_d1.2071237
X-RAY DIFFRACTIONf_dihedral_angle_d12.817332
X-RAY DIFFRACTIONf_chiral_restr0.054148
X-RAY DIFFRACTIONf_plane_restr0.005168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0563-2.11680.26861360.28252563X-RAY DIFFRACTION92
2.1168-2.18510.23391440.21672747X-RAY DIFFRACTION100
2.1851-2.26320.23651460.20082797X-RAY DIFFRACTION100
2.2632-2.35380.24951510.17162785X-RAY DIFFRACTION100
2.3538-2.46090.18571490.16232816X-RAY DIFFRACTION100
2.4609-2.59070.18671400.15832737X-RAY DIFFRACTION100
2.5907-2.7530.17291480.14672781X-RAY DIFFRACTION100
2.753-2.96550.16271490.14362799X-RAY DIFFRACTION100
2.9655-3.26390.19671380.16182788X-RAY DIFFRACTION100
3.2639-3.7360.17641430.15012795X-RAY DIFFRACTION100
3.736-4.70630.1871500.17412805X-RAY DIFFRACTION100
4.7063-48.1750.27041500.24412791X-RAY DIFFRACTION100
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)
11.25730.0776-0.41661.3739-0.25581.2486-0.0341-0.01480.08840.0472-0.0859-0.0650.0234-0.0201-0.09320.04070.01880.00110.02720.0320.27961.36296.2872192.2606
20.12220.02750.42630.00720.07961.6896-0.0371-0.21460.11910.1965-0.26880.20340.7775-0.03570.2311.69230.10330.02471.3171-0.06890.6072-2.1022-8.061116.1676
33.3593-0.6843-0.06595.3301-0.8353.3830.06740.22790.1434-0.1330.3335-0.8821-0.03490.6461-0.28830.5918-0.0076-0.01281.2094-0.16480.8443-12.9936-15.961521.3989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 27 THROUGH 125 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 126 THROUGH 200 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 201 THROUGH 210 )

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