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- PDB-2opd: Structure of the Neisseria meningitidis minor Type IV pilin, PilX -

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Basic information

Entry
Database: PDB / ID: 2opd
TitleStructure of the Neisseria meningitidis minor Type IV pilin, PilX
ComponentsPilX
KeywordsCELL ADHESION / Neisseria meningitidis / type IV pilin / PilX / minor pilin / bacterial pathogenesis / adhesion / aggregation / filament
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / membrane
Similarity search - Function
Fructose-1,6-Bisphosphatase; Chain A, domain 1 - #20 / Minor type IV pilin, PilX-like / Minor type IV pilin, PilX-like superfamily / Minor type IV pilin, PilX / Bacterial general secretion pathway protein G-type pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / Fructose-1,6-Bisphosphatase; Chain A, domain 1 ...Fructose-1,6-Bisphosphatase; Chain A, domain 1 - #20 / Minor type IV pilin, PilX-like / Minor type IV pilin, PilX-like superfamily / Minor type IV pilin, PilX / Bacterial general secretion pathway protein G-type pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDyer, D.H. / Helaine, S. / Pelicic, V. / Forest, K.T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: 3D structure/function analysis of PilX reveals how minor pilins can modulate the virulence properties of type IV pili.
Authors: Helaine, S. / Dyer, D.H. / Nassif, X. / Pelicic, V. / Forest, K.T.
History
DepositionJan 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PilX
B: PilX


Theoretical massNumber of molelcules
Total (without water)28,8292
Polymers28,8292
Non-polymers00
Water1,35175
1
A: PilX


Theoretical massNumber of molelcules
Total (without water)14,4141
Polymers14,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PilX


Theoretical massNumber of molelcules
Total (without water)14,4141
Polymers14,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.128, 83.366, 105.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsData suggest the monomer assembles within the type IV pilus filament, probably replacing one of the major subunits in the helical assembly.

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Components

#1: Protein PilX


Mass: 14414.378 Da / Num. of mol.: 2
Fragment: residues 29-152, plus four N-terminal residues from the expression construct
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: 8013 / Gene: pilX / Plasmid: pMAL-p2X / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0U1RIH2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein at 7 mg/ml in 25 mM KCl, 50 mM Hepes, pH 7.5 was mixed in a 1:1 ratio with unbuffered 4 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER PROTEUM / Detector: CCD / Date: Jun 2, 2005 / Details: Montel 200
RadiationMonochromator: graded multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 10281 / % possible obs: 99.8 % / Redundancy: 8.6 % / Biso Wilson estimate: 58.6 Å2 / Rsym value: 0.074 / Χ2: 0.957 / Net I/σ(I): 17.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 6.3 / Num. unique all: 999 / Rsym value: 0.277 / Χ2: 0.912 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
PROTEUM PLUSPLUSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P43 space group PilX

Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / SU B: 18.396 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.545 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 510 5 %RANDOM
Rwork0.204 ---
obs0.205 9740 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.283 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.65 Å2
Refine analyzeLuzzati coordinate error free: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 0 75 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221948
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9542624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8135240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32924.77388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52915352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.993158
X-RAY DIFFRACTIONr_chiral_restr0.1170.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021458
X-RAY DIFFRACTIONr_nbd_refined0.2450.3929
X-RAY DIFFRACTIONr_nbtor_refined0.3250.51341
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.5147
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.325
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3290.54
X-RAY DIFFRACTIONr_mcbond_it0.6641.51230
X-RAY DIFFRACTIONr_mcangle_it1.09721928
X-RAY DIFFRACTIONr_scbond_it1.8583825
X-RAY DIFFRACTIONr_scangle_it2.6424.5696
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 43 -
Rwork0.25 638 -
obs-681 91.29 %

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