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- PDB-6p2t: BshB from Bacillus subtilis complexed with citrate -

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Basic information

Entry
Database: PDB / ID: 6p2t
TitleBshB from Bacillus subtilis complexed with citrate
ComponentsN-acetyl-alpha-D-glucosaminyl L-malate deacetylase 1
KeywordsHYDROLASE / Bacillithiol / deacetylase / metal-dependent
Function / homology
Function and homology information


bacillithiol biosynthetic process / deacetylase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / metal ion binding
Similarity search - Function
Bacillithiol biosynthesis deacetylase, BshB1 / LmbE-like / N-acetylglucosaminyl phosphatidylinositol deacetylase-related / Putative deacetylase LmbE-like domain superfamily / GlcNAc-PI de-N-acetylase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / N-acetyl-alpha-D-glucosaminyl L-malate deacetylase 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.853 Å
AuthorsCook, P.D. / Meloche, C.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Protein Sci. / Year: 2020
Title: X-ray crystallographic structure of BshB, the zinc-dependent deacetylase involved in bacillithiol biosynthesis.
Authors: Woodward, R.L. / Castleman, M.M. / Meloche, C.E. / Karpen, M.E. / Carlson, C.G. / Yobi, W.H. / Jepsen, J.C. / Lewis, B.W. / Zarnosky, B.N. / Cook, P.D.
History
DepositionMay 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetyl-alpha-D-glucosaminyl L-malate deacetylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1595
Polymers28,6871
Non-polymers4734
Water2,954164
1
A: N-acetyl-alpha-D-glucosaminyl L-malate deacetylase 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)174,95630
Polymers172,1206
Non-polymers2,83624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_635-y+1,x-y-2,z1
crystal symmetry operation3_865-x+y+3,-x+1,z1
crystal symmetry operation10_635y+5/3,x-5/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_765-x+8/3,-x+y+4/3,-z+1/31
Buried area25860 Å2
ΔGint-384 kcal/mol
Surface area48980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.538, 98.538, 184.877
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-154-

PHE

21A-520-

HOH

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Components

#1: Protein N-acetyl-alpha-D-glucosaminyl L-malate deacetylase 1 / GlcNAc-Mal deacetylase 1


Mass: 28686.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: bshB1, jojG, ypjG, BSU22470 / Production host: Escherichia coli (E. coli)
References: UniProt: P42981, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.01 Å3/Da / Density % sol: 63.29 % / Description: parallelogram plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 3350, 100 mM sodium citrate tribasic, 10 mM HEPES, 25 mM NaCl, pH 8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 1.853→77.49 Å / Num. obs: 29650 / % possible obs: 100 % / Redundancy: 14.4 % / Rpim(I) all: 0.029 / Rrim(I) all: 0.109 / Rsym value: 0.105 / Net I/av σ(I): 5.3 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.853-1.9514.81.4850.56328442770.3991.5381.4852.8100
1.95-2.0714.90.8380.85984740290.2250.8680.8385100
2.07-2.2114.90.481.45695638280.1280.4970.488.2100
2.21-2.3914.90.3082.25316035770.0820.3180.30811.4100
2.39-2.6214.80.2083.34859332830.0560.2150.20814.7100
2.62-2.9314.50.1225.74310329670.0330.1270.12220.9100
2.93-3.3813.70.0788.63631926420.0220.0810.07829.5100
3.38-4.1413.10.05710.92953922570.0160.0590.05739100
4.14-5.8612.80.04912.82271017680.0140.0510.04942.8100
5.86-62.703120.04712.21228410220.0140.050.04741.999.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IXD

2ixd


Resolution: 1.853→77.48 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.55 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.104
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 1445 4.9 %RANDOM
Rwork0.1715 ---
obs0.1732 28202 99.97 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 119.46 Å2 / Biso mean: 36.579 Å2 / Biso min: 21.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20.56 Å2-0 Å2
2--1.13 Å2-0 Å2
3----3.65 Å2
Refinement stepCycle: final / Resolution: 1.853→77.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 28 164 1995
Biso mean--63.25 45.96 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131914
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171804
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.6382587
X-RAY DIFFRACTIONr_angle_other_deg1.3141.5834196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8755243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87422.28392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2815345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9621511
X-RAY DIFFRACTIONr_chiral_restr0.0670.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022161
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02392
LS refinement shellResolution: 1.853→1.901 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 120 -
Rwork0.263 2054 -
all-2174 -
obs--100 %

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