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- PDB-5mkd: Crystal structure of Bacillus subtilis Ywea -

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Basic information

Entry
Database: PDB / ID: 5mkd
TitleCrystal structure of Bacillus subtilis Ywea
ComponentsYwea
KeywordsUNKNOWN FUNCTION / bacterial hydrophobin
Function / homology
Function and homology information


extracellular region
Similarity search - Function
: / Immunoglobulin-like - #3490 / YuaB-like / YuaB-like superfamily / Biofilm surface layer A / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein / Probable biofilm-surface layer protein B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsCarrington, J. / van Aalten, D.
CitationJournal: To Be Published
Title: Crystal structure of Bacillus subtilis Ywea
Authors: Carrington, J. / van Aalten, D.
History
DepositionDec 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ywea
B: Ywea
C: Ywea
D: Ywea


Theoretical massNumber of molelcules
Total (without water)54,1774
Polymers54,1774
Non-polymers00
Water41423
1
A: Ywea


Theoretical massNumber of molelcules
Total (without water)13,5441
Polymers13,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ywea


Theoretical massNumber of molelcules
Total (without water)13,5441
Polymers13,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ywea


Theoretical massNumber of molelcules
Total (without water)13,5441
Polymers13,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ywea


Theoretical massNumber of molelcules
Total (without water)13,5441
Polymers13,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.405, 128.306, 84.327
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

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Components

#1: Protein
Ywea


Mass: 13544.295 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_2102 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164UMC7, UniProt: P39632*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: See manuscript

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.51→49.27 Å / Num. all: 118718 / Num. obs: 22769 / % possible obs: 99.5 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.035 / Rrim(I) all: 0.082 / Net I/σ(I): 16.1
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 1.6 / Num. measured obs: 22769 / Num. unique all: 2182 / CC1/2: 0.652 / Rpim(I) all: 0.483 / Rrim(I) all: 1.132 / % possible all: 97.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→49.27 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.075 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.391 / ESU R Free: 0.276
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 480 2.1 %RANDOM
Rwork0.208 ---
obs0.2092 22289 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 131.28 Å2 / Biso mean: 56.558 Å2 / Biso min: 30.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2--0.45 Å20 Å2
3----2.06 Å2
Refinement stepCycle: final / Resolution: 2.51→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 0 23 3823
Biso mean---43.71 -
Num. residues----494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023868
X-RAY DIFFRACTIONr_bond_other_d0.0010.023765
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9715255
X-RAY DIFFRACTIONr_angle_other_deg0.77238664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8225491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20424.472161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58715667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2791524
X-RAY DIFFRACTIONr_chiral_restr0.0850.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02830
LS refinement shellResolution: 2.51→2.575 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 35 -
Rwork0.353 1579 -
all-1614 -
obs--96.42 %

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