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- PDB-5v23: SeMet crystal structure of the Neisseria meningitidis non-core mi... -

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Basic information

Entry
Database: PDB / ID: 5v23
TitleSeMet crystal structure of the Neisseria meningitidis non-core minor pilin PilV in the orthorhombic form
ComponentsType IV pilin protein
KeywordsCELL ADHESION / pilin / minor pilin / type IV pili / Neisseria meningitidis
Function / homologyType IV pilus non-core minor pilin PilE-like / Type IV minor pilin ComP, DNA uptake sequence receptor / type IV pilus assembly / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / Type IV pilin protein
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.956 Å
AuthorsKolappan, S. / Craig, L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP125959 Canada
CitationJournal: To Be Published
Title: SeMet structure of the non-core minor pilin PilV from Neisseria meningitidis in the orthorhombic form
Authors: Kolappan, S. / Craig, L.
History
DepositionMar 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Type IV pilin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4004
Polymers11,1241
Non-polymers2763
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)21.794, 39.343, 109.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Type IV pilin protein


Mass: 11124.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: A6L27_01160 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B1ZB31
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 8000, ammonium chloride, sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.976047, 0.979412
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 29, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9760471
20.9794121
ReflectionResolution: 1.956→54.81 Å / Num. obs: 7263 / % possible obs: 98.7 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.026 / Net I/σ(I): 23.9
Reflection shellResolution: 1.96→2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 5.5 / Num. unique all: 442 / CC1/2: 0.981 / Rpim(I) all: 0.129 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.956→37.03 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.24
RfactorNum. reflection% reflection
Rfree0.2545 371 5.14 %
Rwork0.1846 --
obs0.1884 7217 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.956→37.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms773 0 18 73 864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007824
X-RAY DIFFRACTIONf_angle_d0.9321111
X-RAY DIFFRACTIONf_dihedral_angle_d16.705502
X-RAY DIFFRACTIONf_chiral_restr0.048120
X-RAY DIFFRACTIONf_plane_restr0.005146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9556-2.23850.26561080.18052181X-RAY DIFFRACTION97
2.2385-2.82010.28881250.20282273X-RAY DIFFRACTION99
2.8201-37.03650.23741380.17752392X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.3261 Å / Origin y: 15.2013 Å / Origin z: 70.6041 Å
111213212223313233
T0.1712 Å20.0098 Å20.0354 Å2-0.1332 Å20.0162 Å2--0.1255 Å2
L0.6047 °20.535 °2-0.2072 °2-2.1784 °2-0.5477 °2--0.8871 °2
S-0.0482 Å °0.034 Å °-0.0789 Å °-0.4822 Å °-0.0018 Å °-0.1802 Å °-0.0291 Å °-0.0256 Å °0.0009 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 25 through 122 )

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