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- PDB-6tzp: W96F Oxalate Decarboxylase (B. subtilis) -

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Basic information

Entry
Database: PDB / ID: 6tzp
TitleW96F Oxalate Decarboxylase (B. subtilis)
ComponentsOxalate decarboxylase
KeywordsLYASE / Oxalate Decarboxylase / electron transfer / Bacillus subtilis
Function / homology
Function and homology information


oxalate decarboxylase / oxalate decarboxylase activity / oxalate metabolic process / outer membrane-bounded periplasmic space / lyase activity / metal ion binding / cytoplasm
Similarity search - Function
Bicupin, oxalate decarboxylase/oxidase / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
: / Oxalate decarboxylase / Oxalate decarboxylase OxdC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsPastore, A.J. / Burg, M.J. / Twahir, U.T. / Bruner, S.D. / Angerhofer, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1213440 United States
Citation
Journal: J.Biol.Chem. / Year: 2021
Title: Oxalate decarboxylase uses electron hole hopping for catalysis.
Authors: Pastore, A.J. / Teo, R.D. / Montoya, A. / Burg, M.J. / Twahir, U.T. / Bruner, S.D. / Beratan, D.N. / Angerhofer, A.
#1: Journal: J Struct Biol / Year: 2021
Title: Practical considerations for using K3 cameras in CDS mode for high-resolution and high-throughput single particle cryo-EM.
Authors: Ming Sun / Caleigh M Azumaya / Eric Tse / David P Bulkley / Matthew B Harrington / Glenn Gilbert / Adam Frost / Daniel Southworth / Kliment A Verba / Yifan Cheng / David A Agard /
Abstract: Detector technology plays a pivotal role in high-resolution and high-throughput cryo-EM structure determination. Compared with the first-generation, single-electron counting direct detection camera ...Detector technology plays a pivotal role in high-resolution and high-throughput cryo-EM structure determination. Compared with the first-generation, single-electron counting direct detection camera (Gatan K2), the latest K3 camera is faster, larger, and now offers a correlated-double sampling mode (CDS). Importantly this results in a higher DQE and improved throughput compared to its predecessor. In this study, we focused on optimizing camera data collection parameters for daily use within a cryo-EM facility and explored the balance between throughput and resolution. In total, eight data sets of murine heavy-chain apoferritin were collected at different dose rates and magnifications, using 9-hole image shift data collection strategies. The performance of the camera was characterized by the quality of the resultant 3D reconstructions. Our results demonstrated that the Gatan K3 operating in CDS mode outperformed standard (nonCDS) mode in terms of reconstruction resolution in all tested conditions with 8 electrons per pixel per second being the optimal dose rate. At low magnification (64kx) we were able to achieve reconstruction resolutions of 149% of the physical Nyquist limit (1.8 Å with a 1.346 Å physical pixel size). Low magnification allows more particles to be collected per image, aiding analysis of heterogeneous samples requiring large data sets. At moderate magnification (105kx, 0.834 Å physical pixel size) we achieved a resolution of 1.65 Å within 8-h of data collection, a condition optimal for achieving high-resolution on well behaved samples. Our results also show that for an optimal sample like apoferritin, one can achieve better than 2.5 Å resolution with 5 min of data collection. Together, our studies validate the most efficient ways of imaging protein complexes using the K3 direct detector and will greatly benefit the cryo-EM community.
History
DepositionAug 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 11, 2023Group: 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: Oxalate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6923
Polymers43,5821
Non-polymers1102
Water4,558253
1
A: Oxalate decarboxylase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)262,15018
Polymers261,4916
Non-polymers65912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area45780 Å2
ΔGint-347 kcal/mol
Surface area68960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.073, 155.073, 123.079
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-707-

HOH

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Components

#1: Protein Oxalate decarboxylase / Cupin domain-containing protein


Mass: 43581.867 Da / Num. of mol.: 1 / Mutation: W96F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3145, ETL41_08750 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A162QMS4, UniProt: O34714*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.26 Å3/Da / Density % sol: 62.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20 mM Tris, 80 mM sodium chloride, 10 mM arginine, 10 mM glutamate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.716→36.247 Å / Num. all: 865952 / Num. obs: 60461 / % possible obs: 99.89 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.1221 / Net I/σ(I): 19.32
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.266 / Mean I/σ(I) obs: 2.31 / Num. unique all: 81901 / Num. unique obs: 59982 / CC1/2: 0.49 / % possible all: 99.22

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VG3

5vg3


Resolution: 1.72→31.865 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1787 2999 4.96 %
Rwork0.1606 57462 -
obs0.1615 60461 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.08 Å2 / Biso mean: 17.1368 Å2 / Biso min: 6.93 Å2
Refinement stepCycle: final / Resolution: 1.72→31.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 2 253 3252
Biso mean--13.02 25.28 -
Num. residues----377
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.72-1.74380.3051230.2826264697
1.7438-1.77380.25531370.23382702100
1.7738-1.80610.23551380.20082744100
1.8061-1.84080.21911340.17952748100
1.8408-1.87840.20331420.16922700100
1.8784-1.91920.20461450.16942730100
1.9192-1.96390.18041350.17172737100
1.9639-2.0130.21671480.16212716100
2.013-2.06740.18071550.14962701100
2.0674-2.12820.16481280.1512771100
2.1282-2.19690.18171520.1482704100
2.1969-2.27540.17331430.14612730100
2.2754-2.36650.18191500.15872710100
2.3665-2.47410.18111510.16012741100
2.4741-2.60450.18731460.16662732100
2.6045-2.76760.20521440.16792739100
2.7676-2.98120.17841510.16692755100
2.9812-3.28090.17671500.15782748100
3.2809-3.7550.16281510.15122745100
3.755-4.72840.13181330.13272800100
4.7284-31.8650.17871430.16062863100
Refinement TLS params.Method: refined / Origin x: 22.9327 Å / Origin y: 3.1967 Å / Origin z: 16.6832 Å
111213212223313233
T0.0836 Å2-0.0044 Å2-0.0094 Å2-0.0912 Å2-0.0019 Å2--0.085 Å2
L0.0798 °20.0298 °20.0324 °2-0.0737 °2-0.0161 °2--0.0584 °2
S-0.0046 Å °-0.0255 Å °0.0041 Å °0.0154 Å °0.0073 Å °-0.0298 Å °0.0067 Å °0.0182 Å °-0.0043 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 382
2X-RAY DIFFRACTION1allA1383 - 1384
3X-RAY DIFFRACTION1allC1 - 256

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