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- PDB-4hsq: Crystal Structure of Domains D2 and D3 of the Major Pilin SpaD fr... -

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Basic information

Entry
Database: PDB / ID: 4hsq
TitleCrystal Structure of Domains D2 and D3 of the Major Pilin SpaD from Corynebacterium diphtheriae
ComponentsPutative fimbrial subunit
KeywordsCELL ADHESION / CnaA/CnaB domains / Major Pilin / Isopeptide bond via Lys-Asn side chains
Function / homology
Function and homology information


carbohydrate metabolic process / membrane / metal ion binding
Similarity search - Function
Sgo0707-like, N2 domain / Sgo0707 N2 domain / : / Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Sgo0707-like, N2 domain / Sgo0707 N2 domain / : / Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.87 Å
AuthorsPaterson, N.G. / Kang, H.J. / Baker, E.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: A slow-forming isopeptide bond in the structure of the major pilin SpaD from Corynebacterium diphtheriae has implications for pilus assembly.
Authors: Kang, H.J. / Paterson, N.G. / Kim, C.U. / Middleditch, M. / Chang, C. / Ton-That, H. / Baker, E.N.
History
DepositionOct 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Jun 25, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative fimbrial subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5792
Polymers30,5391
Non-polymers401
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.992, 81.335, 92.371
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 Putative fimbrial subunit


Mass: 30539.113 Da / Num. of mol.: 1 / Fragment: Domains D2-3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: ATCC 700971 / NCTC 13129 / Biotype gravis / Gene: DIP0235 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6NK05
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 47% 2-methyl-2,4-pentanediol, 2% t-butanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 31, 2009
RadiationMonochromator: Osmic optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→19.86 Å / Num. all: 23142 / Num. obs: 23142 / % possible obs: 99.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 39.8 % / Biso Wilson estimate: 22.07 Å2 / Rmerge(I) obs: 0.087
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 35.6 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 9.6 / Num. unique all: 3255 / % possible all: 97.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.87→19.86 Å / Cor.coef. Fo:Fc: 0.9626 / Cor.coef. Fo:Fc free: 0.9501 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1899 1184 5.12 %RANDOM
Rwork0.1573 ---
all0.159 23113 --
obs0.159 23113 --
Displacement parametersBiso mean: 26.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.1934 Å20 Å20 Å2
2--0.1106 Å20 Å2
3---0.0828 Å2
Refine analyzeLuzzati coordinate error obs: 0.172 Å
Refinement stepCycle: LAST / Resolution: 1.87→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 1 346 2457
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012143HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.142891HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1029SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes301HARMONIC5
X-RAY DIFFRACTIONt_it2143HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.38
X-RAY DIFFRACTIONt_other_torsion2.73
X-RAY DIFFRACTIONt_chiral_improper_torsion291SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2715SEMIHARMONIC4
LS refinement shellResolution: 1.87→1.95 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2297 149 5.45 %
Rwork0.1808 2584 -
all0.1835 2733 -

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