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- PDB-4wfw: The crystal structure of Dickeya dadantii GspB from the type 2 se... -

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Basic information

Entry
Database: PDB / ID: 4wfw
TitleThe crystal structure of Dickeya dadantii GspB from the type 2 secretion system
ComponentsGeneral secretion pathway protein B
KeywordsSTRUCTURAL PROTEIN / Type 2 Secretion System / GspB
Function / homologyType II secretion system protein GspB / Type II secretion system protein B / type II protein secretion system complex / protein processing / membrane => GO:0016020 / plasma membrane / General secretion pathway protein B
Function and homology information
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRycroft, P.B. / Pickersgill, R.W. / Shevchik, V.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I013334/1 United Kingdom
CitationJournal: To Be Published
Title: The crystal structure of Dickeya dadantii GspB from the type 2 secretion system
Authors: Rycroft, P.B.
History
DepositionSep 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model / Author supporting evidence
Category: atom_site / pdbx_audit_support / pdbx_validate_close_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: General secretion pathway protein B


Theoretical massNumber of molelcules
Total (without water)9,9221
Polymers9,9221
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.210, 36.210, 131.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein General secretion pathway protein B


Mass: 9921.942 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (strain 3937) (bacteria)
Strain: 3937 / Gene: outB, Dda3937_02412 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01563
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: initial hit from nano drop. Scaled up using whisker streak seeding. 0.2M MgCl, 0.1M Tris, 30% w/v PEG4000, pH8.5
PH range: 8.4-8.6 / Temp details: Air Conditioned room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→36.03 Å / Num. obs: 6380 / % possible obs: 99.2 % / Redundancy: 8.9 % / Net I/σ(I): 30.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0085refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3oss

3oss


Resolution: 2.05→34.91 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.881 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25421 591 10.1 %RANDOM
Rwork0.20853 ---
obs0.21303 5276 97.39 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.749 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.05→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms661 0 0 15 676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02685
X-RAY DIFFRACTIONr_bond_other_d0.0030.02616
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.959933
X-RAY DIFFRACTIONr_angle_other_deg0.9531427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.603584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0882534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02415103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.034153
X-RAY DIFFRACTIONr_chiral_restr0.0940.296
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021790
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02155
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6653.22339
X-RAY DIFFRACTIONr_mcbond_other1.6663.206338
X-RAY DIFFRACTIONr_mcangle_it2.6084.805422
X-RAY DIFFRACTIONr_mcangle_other2.6054.821423
X-RAY DIFFRACTIONr_scbond_it1.863.428346
X-RAY DIFFRACTIONr_scbond_other1.8593.44347
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9115.069512
X-RAY DIFFRACTIONr_long_range_B_refined4.6826.228754
X-RAY DIFFRACTIONr_long_range_B_other4.67726.296755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 40 -
Rwork0.291 356 -
obs--93.62 %
Refinement TLS params.Method: refined / Origin x: 15.449 Å / Origin y: 9.637 Å / Origin z: 41.627 Å
111213212223313233
T0.2035 Å20.0377 Å20.0463 Å2-0.1388 Å20.0074 Å2--0.0388 Å2
L4.5042 °21.2491 °2-1.1685 °2-8.6324 °2-0.0262 °2--4.0744 °2
S-0.1117 Å °0.4153 Å °-0.1042 Å °-0.8122 Å °0.0432 Å °-0.5553 Å °0.0657 Å °0.3929 Å °0.0685 Å °

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