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- PDB-2ope: Crystal structure of the Neisseria meningitidis minor Type IV pil... -

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Basic information

Entry
Database: PDB / ID: 2ope
TitleCrystal structure of the Neisseria meningitidis minor Type IV pilin, PilX, in space group P43
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 / Combination of SAD, Mol. Replacement / Resolution: 2.4 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PilX
B: PilX
C: PilX
D: PilX


Theoretical massNumber of molelcules
Total (without water)57,6584
Polymers57,6584
Non-polymers00
Water3,261181
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
3
C: PilX


Theoretical massNumber of molelcules
Total (without water)14,4141
Polymers14,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 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)76.836, 76.836, 89.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
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.: 4
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


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG 8K, 120 mM LiSO4, 100 mM Bis Tris, pH 6.5, 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: May 18, 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: 2.4→25 Å / Num. obs: 20280 / % possible obs: 98.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.072 / Χ2: 0.964 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.493.10.24317940.7187.2
2.49-2.593.80.21820080.7398.4
2.59-2.75.40.1820440.793100
2.7-2.847.20.16520390.82100
2.84-3.027.40.1420600.934100
3.02-3.267.40.10720301.036100
3.26-3.587.40.07220621.05100
3.58-4.17.40.05720581.024100
4.1-5.167.40.04620790.976100
5.16-257.20.05521061.19100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
PROTEUM PLUSPLUSdata collection
HKL-2000data reduction
SOLVEfor sad phasingphasing
RESOLVEfor sad phasingphasing
RefinementMethod to determine structure: Combination of SAD, Mol. Replacement
Resolution: 2.4→25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 16.586 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.504 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The P43 structure was initially solved by SAD phasing using SeMet-substituted PilX. This initial model was used for molecular replacement to solve the companion C2221 structure (2OPD) for ...Details: The P43 structure was initially solved by SAD phasing using SeMet-substituted PilX. This initial model was used for molecular replacement to solve the companion C2221 structure (2OPD) for which the data are substantially better. After that structure was refined, it was used as the molecular replacement model for structure solution of the P43 structure using native data collected on a rotating anode.
RfactorNum. reflection% reflectionSelection details
Rfree0.27893 1033 5.1 %RANDOM
Rwork0.20794 ---
obs0.21156 19111 98.61 %-
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: 47.078 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refine analyzeLuzzati coordinate error free: 0.303 Å
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 0 181 3803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223693
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9544976
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09124.534161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93415651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7531516
X-RAY DIFFRACTIONr_chiral_restr0.1110.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022748
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.31839
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.52540
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.5345
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.376
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.02722349
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59833679
X-RAY DIFFRACTIONr_scbond_it1.15921538
X-RAY DIFFRACTIONr_scangle_it1.63431297
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 68 -
Rwork0.217 1201 -
obs-1269 86.09 %

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