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- PDB-4hss: Structure of the Full-Length Major Pilin SpaD from Corynebacteriu... -

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Basic information

Entry
Database: PDB / ID: 4hss
TitleStructure of the Full-Length Major Pilin SpaD from Corynebacterium diphtheriae
ComponentsPutative fimbrial subunit
KeywordsCELL ADHESION / CnaA/CnaB folded domains / Major pilin polymer / Homopolymer / Isopeptide bonding between Lys and Asn sidechains
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
Revision 1.3Sep 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative fimbrial subunit
B: Putative fimbrial subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3234
Polymers94,2432
Non-polymers802
Water5,044280
1
A: Putative fimbrial subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1622
Polymers47,1221
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative fimbrial subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1622
Polymers47,1221
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.828, 56.791, 435.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsSpaD subunits covalently linked by sortase-catalysed isopeptide bond between C-terminal sortase motif Thr carboxyl and epsilon amino group of Lys 179 in D1 of next monomer. Chains A and B are arranged in the predicted polymer orientation and this continues throughout the crystal via symmetry operations.

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Components

#1: Protein Putative fimbrial subunit


Mass: 47121.578 Da / Num. of mol.: 2 / Fragment: Domains D1-D3
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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15% PEG 600, 0.2M imidazole-malate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 5, 2009
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.5→29.06 Å / Num. all: 27956 / Num. obs: 27956 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 55.39 Å2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4066 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HSQ

4hsq


Resolution: 2.5→28.36 Å / Cor.coef. Fo:Fc: 0.9073 / Cor.coef. Fo:Fc free: 0.8776 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1405 5.03 %RANDOM
Rwork0.1873 ---
all0.1904 27924 --
obs0.1904 27924 --
Displacement parametersBiso mean: 53.75 Å2
Baniso -1Baniso -2Baniso -3
1--16.4399 Å20 Å20 Å2
2---5.0054 Å20 Å2
3---21.4454 Å2
Refine analyzeLuzzati coordinate error obs: 0.311 Å
Refinement stepCycle: LAST / Resolution: 2.5→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6209 0 2 280 6491
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016314HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.238533HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2988SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes187HARMONIC2
X-RAY DIFFRACTIONt_gen_planes892HARMONIC5
X-RAY DIFFRACTIONt_it6314HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.46
X-RAY DIFFRACTIONt_other_torsion3.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion860SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6844SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3726 119 4.1 %
Rwork0.2374 2783 -
all0.2429 2902 -

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