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- PDB-5v8e: Structure of Bacillus cereus PatB1 -

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Basic information

Entry
Database: PDB / ID: 5v8e
TitleStructure of Bacillus cereus PatB1
ComponentsBacillus cereus PatB1
KeywordsUNKNOWN FUNCTION / acetyltransferase / cell wall / SGNH hydrolase-like / TRANSFERASE
Function / homologyDHHW protein / DHHW protein / membrane / CITRIC ACID / DI(HYDROXYETHYL)ETHER / AlgX/AlgJ SGNH hydrolase-like domain-containing protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSychantha, D. / Little, D.J. / Chapman, R.N. / Boons, G.J. / Robinson, H. / Howell, P.L. / Clarke, A.J.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: PatB1 is an O-acetyltransferase that decorates secondary cell wall polysaccharides.
Authors: Sychantha, D. / Little, D.J. / Chapman, R.N. / Boons, G.J. / Robinson, H. / Howell, P.L. / Clarke, A.J.
History
DepositionMar 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 23, 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: Bacillus cereus PatB1
B: Bacillus cereus PatB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5309
Polymers71,6122
Non-polymers9187
Water2,900161
1
A: Bacillus cereus PatB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4266
Polymers35,8061
Non-polymers6195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bacillus cereus PatB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1043
Polymers35,8061
Non-polymers2982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.760, 133.760, 87.311
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Bacillus cereus PatB1 / Uncharacterized protein


Mass: 35806.043 Da / Num. of mol.: 2 / Fragment: UNP residues 88-396 / Mutation: K232A, K233A, E234A, K300A, Q301A, K302A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 10987 / NRS 248) (bacteria)
Strain: ATCC 10987 / NRS 248 / Gene: BCE_0974 / Production host: Escherichia coli (E. coli) / Variant (production host): T7 Shuffle / References: UniProt: Q73CU0
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.15 Å3/Da / Density % sol: 60.97 % / Description: Hexagonal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Sodium Citrate:Citric Acid pH 5.5, 40% (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 45198 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 10
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 10 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→43.783 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2415 2283 5.08 %
Rwork0.1988 --
obs0.201 44966 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→43.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4908 0 61 161 5130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085092
X-RAY DIFFRACTIONf_angle_d1.1296916
X-RAY DIFFRACTIONf_dihedral_angle_d15.5511810
X-RAY DIFFRACTIONf_chiral_restr0.043738
X-RAY DIFFRACTIONf_plane_restr0.005901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.24780.311230.30272678X-RAY DIFFRACTION100
2.2478-2.30010.34461440.2762646X-RAY DIFFRACTION100
2.3001-2.35770.27021450.24032668X-RAY DIFFRACTION100
2.3577-2.42140.28761440.23642659X-RAY DIFFRACTION99
2.4214-2.49260.25371710.23512610X-RAY DIFFRACTION99
2.4926-2.57310.28871270.23562668X-RAY DIFFRACTION100
2.5731-2.6650.28921390.22782659X-RAY DIFFRACTION99
2.665-2.77170.29481490.23282630X-RAY DIFFRACTION100
2.7717-2.89780.2751300.23062673X-RAY DIFFRACTION99
2.8978-3.05060.29141440.23442649X-RAY DIFFRACTION99
3.0506-3.24170.24631450.22532657X-RAY DIFFRACTION99
3.2417-3.49190.27971630.21082671X-RAY DIFFRACTION100
3.4919-3.84310.20671430.19132655X-RAY DIFFRACTION100
3.8431-4.39870.21241580.16442683X-RAY DIFFRACTION100
4.3987-5.54020.21581190.15632720X-RAY DIFFRACTION100
5.5402-43.79190.18671390.16722757X-RAY DIFFRACTION99

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