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- PDB-4v1j: Structure of Neisseria meningitidis Major Pillin -

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Basic information

Entry
Database: PDB / ID: 4v1j
TitleStructure of Neisseria meningitidis Major Pillin
ComponentsFIMBRIAL PROTEIN
KeywordsCELL ADHESION / TYPE IV PILLUS
Function / homology
Function and homology information


pilus / cell adhesion / membrane
Similarity search - Function
Glycoprotein, Type 4 Pilin / Glycoprotein, Type 4 Pilin / Fimbrial protein pilin / Pilin (bacterial filament) / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNEISSERIA MENINGITIDIS MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsHarding, R.J. / Exley, R. / Tang, C.M. / Caesar, J.J.E. / Lea, S.M.
CitationJournal: To be Published
Title: Tstructure of Neisseria Meningitidis Major Pillin
Authors: Harding, R.J. / Exley, R. / Tang, C.M. / Caesar, J.J.E. / Lea, S.M.
History
DepositionSep 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / atom_site_anisotrop / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIMBRIAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2674
Polymers15,1081
Non-polymers1603
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.060, 105.060, 23.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-2070-

HOH

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Components

#1: Protein FIMBRIAL PROTEIN / PILIN


Mass: 15107.851 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS MC58 (bacteria) / Gene: PILE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P05431
#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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsETHANOLAMINE (EDO): N/A
Sequence detailsDATABASE CONTAINS SIGNAL SEQUENCE AND 24 ADDITIONAL RESIDUES, GPM COMES FROM EXPRESSION VECTOR

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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: 2.43 Å3/Da / Density % sol: 49.42 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M SODIUM HEPES PH7.5, 45% V/V PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.984
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.43→23.06 Å / Num. obs: 27504 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.3
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HI2

2hi2


Resolution: 1.43→23.06 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.927 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.17586 1383 5 %RANDOM
Rwork0.1383 ---
obs0.14023 26116 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: 20.768 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.06 Å20 Å2
2--0.13 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.43→23.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 9 80 1133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021124
X-RAY DIFFRACTIONr_bond_other_d0.0010.021114
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9471530
X-RAY DIFFRACTIONr_angle_other_deg0.8593.0022535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9925157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95225.81443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.17315197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.741154
X-RAY DIFFRACTIONr_chiral_restr0.0940.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021310
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02236
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.99332237
X-RAY DIFFRACTIONr_sphericity_free24.398531
X-RAY DIFFRACTIONr_sphericity_bonded15.4452266
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 121 -
Rwork0.198 1723 -
obs--99.95 %

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