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- PDB-8hpk: Crystal structure of the bacterial oxalate transporter OxlT in an... -

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Basic information

Entry
Database: PDB / ID: 8hpk
TitleCrystal structure of the bacterial oxalate transporter OxlT in an oxalate-bound occluded form
Components
  • Fab fragment Heavy chein
  • Fab fragment Light chain
  • Oxalate:formate antiporter
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / major facilitator superfamily membrane protein transporter / TRANSPORT PROTEIN / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


oxalate transmembrane transporter activity / antiporter activity / monoatomic ion transport / plasma membrane
Similarity search - Function
Oxalate/formate antiporter family transporter / Oxalate/formate antiporter / : / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Immunoglobulins / Immunoglobulin-like ...Oxalate/formate antiporter family transporter / Oxalate/formate antiporter / : / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
OXALATE ION / Oxalate:formate antiporter
Similarity search - Component
Biological speciesOxalobacter formigenes (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShimamura, T. / Hirai, T. / Yamashita, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20H03195 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota.
Authors: Jaunet-Lahary, T. / Shimamura, T. / Hayashi, M. / Nomura, N. / Hirasawa, K. / Shimizu, T. / Yamashita, M. / Tsutsumi, N. / Suehiro, Y. / Kojima, K. / Sudo, Y. / Tamura, T. / Iwanari, H. / ...Authors: Jaunet-Lahary, T. / Shimamura, T. / Hayashi, M. / Nomura, N. / Hirasawa, K. / Shimizu, T. / Yamashita, M. / Tsutsumi, N. / Suehiro, Y. / Kojima, K. / Sudo, Y. / Tamura, T. / Iwanari, H. / Hamakubo, T. / Iwata, S. / Okazaki, K.I. / Hirai, T. / Yamashita, A.
History
DepositionDec 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxalate:formate antiporter
H: Fab fragment Heavy chein
L: Fab fragment Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0804
Polymers92,9923
Non-polymers881
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.950, 233.190, 50.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Oxalate:formate antiporter / OFA / Oxalate:formate antiport protein / Oxalate:formate exchange protein


Mass: 45787.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes (bacteria) / Gene: oxlT / Production host: Escherichia coli (E. coli) / References: UniProt: Q51330
#2: Antibody Fab fragment Heavy chein


Mass: 23610.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody Fab fragment Light chain


Mass: 23594.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 3.71 Å3/Da / Density % sol: 66.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M sodium citrate, pH 5.5, 0.05 M NaCl, 26% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→46.6 Å / Num. obs: 22609 / % possible obs: 92.9 % / Redundancy: 99.8 % / Biso Wilson estimate: 46.98 Å2 / CC1/2: 0.997 / Net I/σ(I): 16.4
Reflection shellResolution: 2.6→2.94 Å / Num. unique obs: 1130 / CC1/2: 0.65

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PW4, 1XF4

1pw4

1xf4


Resolution: 3→21.1 Å / SU ML: 0.3632 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3141
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2783 1859 8.87 %
Rwork0.2369 19091 -
obs0.2406 20950 74.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.17 Å2
Refinement stepCycle: LAST / Resolution: 3→21.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6194 0 6 0 6200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266364
X-RAY DIFFRACTIONf_angle_d0.5848668
X-RAY DIFFRACTIONf_chiral_restr0.0416977
X-RAY DIFFRACTIONf_plane_restr0.00521090
X-RAY DIFFRACTIONf_dihedral_angle_d11.4411875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.3327450.2962467X-RAY DIFFRACTION24.53
3.08-3.170.318590.2896604X-RAY DIFFRACTION30.79
3.17-3.270.3534760.3053767X-RAY DIFFRACTION40.32
3.27-3.390.31621020.26891047X-RAY DIFFRACTION52.83
3.39-3.520.32551150.28361195X-RAY DIFFRACTION62.41
3.52-3.680.30911370.26071402X-RAY DIFFRACTION71.38
3.68-3.880.28731610.24231659X-RAY DIFFRACTION84.77
3.88-4.120.28771790.24341839X-RAY DIFFRACTION94.26
4.12-4.430.24951930.21931973X-RAY DIFFRACTION99.95
4.43-4.880.24861930.20131988X-RAY DIFFRACTION100
4.88-5.570.24821940.20241999X-RAY DIFFRACTION100
5.57-6.970.32141980.24352029X-RAY DIFFRACTION99.96
6.98-21.10.25172070.23822122X-RAY DIFFRACTION99.57
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.426407975415-0.315863043838-0.2007946190740.8373335195230.2850077851010.1759181942670.1386356695760.1936477119450.0547942285461-0.409927472185-0.233182565909-0.06606923839710.0970539449816-0.00805421152825-0.1250406760240.4231048112720.09201463806040.2467655817890.1559793454750.003671128179060.29585288476526.909498036779.32046761277.55902305623
20.77103566046-0.7329248579010.1964797890760.90801509518-0.4340513802680.6382647036890.0427187179744-0.07261372055740.443778410520.0588271178364-0.0397306009211-0.325406606574-0.2101252209580.147256125179-0.5030167922360.214394456887-0.03096362012290.1940482922630.134203305127-0.1215590462750.35190353567434.465746984883.466513343424.1168191674
31.938024991890.93901195937-0.3723704553233.138484239121.300092646133.559542380890.2403362633020.1299499561630.00889230199117-0.0855127929895-0.1975541885130.3046177201810.0645638249219-0.2497300111750.1141037711330.7177767455030.251564121208-0.07829559844280.371930465587-0.09990989596920.26205006401627.411489877738.207917986912.6770314784
41.04078458574-0.2942067074950.03641454473020.228671903374-0.48025762481.505438496220.3293525414090.0637890953283-0.417575888812-0.400248559203-0.0489093057930.01678903014260.8392180301560.1614546417690.02985009790980.7770940165990.119925827661-0.1479364509860.414213563585-0.04153236256530.25967277421428.239087815527.988157477618.135302098
52.93627849956-1.668584596360.8414268142913.810495936462.12967672542.616337815550.159433355863-0.0308822025536-0.686608473987-0.574841737875-0.05135104518820.8323902408450.235136993521-0.408501812774-0.04149552110640.986390838948-0.0681368493086-0.2097655188240.3059827228650.01381525865980.71660613291227.64148811979.3195879401931.4898574462
61.169158354940.198797881408-0.4232086107292.008961934480.3636663568560.5312893115880.0349052509038-0.1770942577350.01163895531160.1941942410290.0706503393117-0.2662210432960.1674154138520.2424308875890.02110984870370.1809406364870.136983390855-0.02736682186210.178161417009-0.06965346629710.10133633089538.088660850945.107543826931.7763267971
70.491472483657-0.7677411383360.1610472310121.65377323015-0.008057134766690.849925726778-0.0168410764698-0.0527395876294-0.2353668787250.2814934664570.06282841946960.3497183101030.3669197773470.02917065485870.1701112738050.3799924457150.1202158930960.1265989543610.2073954139930.009275810285850.27530612260537.945989223727.647592781532.2861285242
85.02859798683-1.31487300844-0.06327347910843.341063753963.802396140995.207406115360.1874324716120.172862390156-0.043385341062-1.011953948850.236676220516-0.4126012700740.338639811210.616833837796-0.3784480607330.744933374060.1474762113140.208945683040.3275318058430.1015545385670.58243735801944.335639505710.922044121836.7551547783
92.75220481502-0.1788876952720.6543334972545.665953156821.555404928980.6083179412840.1162945540070.330039088827-0.525015597784-0.690989691101-0.0747096974823-0.7829037589630.3715416805110.265448299698-0.07644951286820.7814647322210.237451636890.1819407989110.4042325171210.1105913911060.60096236354944.66424312535.6950448719635.3133468294
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 191 )AA11 - 1911 - 181
22chain 'A' and (resid 192 through 405 )AA192 - 405182 - 390
33chain 'H' and (resid 2 through 67 )HC2 - 671 - 66
44chain 'H' and (resid 68 through 139 )HC68 - 13967 - 138
55chain 'H' and (resid 140 through 218 )HC140 - 218139 - 212
66chain 'L' and (resid 1 through 76 )LD1 - 761 - 76
77chain 'L' and (resid 77 through 129 )LD77 - 12977 - 129
88chain 'L' and (resid 130 through 151 )LD130 - 151130 - 151
99chain 'L' and (resid 152 through 215 )LD152 - 215152 - 215

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