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- PDB-6d79: Structure of CysZ, a sulfate permease from Pseudomonas Fragi -

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Basic information

Entry
Database: PDB / ID: 6d79
TitleStructure of CysZ, a sulfate permease from Pseudomonas Fragi
ComponentsSulfate transporter CysZ
KeywordsTRANSPORT PROTEIN / Membrane protein / sulfate translocation / prokaryotic cysteine biosynthesis
Function / homologySulfate transporter CysZ / Sulfate transporter CysZ/Etoposide-induced protein 2.4 / sulfate transmembrane transporter activity / sulfate assimilation / cysteine biosynthetic process / plasma membrane => GO:0005886 / Sulfate transporter CysZ
Function and homology information
Biological speciesPseudomonas fragi A22 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.501 Å
AuthorsSanghai, Z.A. / Liu, Q. / Clarke, O.B. / Banerjee, S. / Rajashankar, K.R. / Hendrickson, W.A. / Mancia, F.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM098617 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM107462 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM095315 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM116799 United States
CitationJournal: Elife / Year: 2018
Title: Structure-based analysis of CysZ-mediated cellular uptake of sulfate.
Authors: Assur Sanghai, Z. / Liu, Q. / Clarke, O.B. / Belcher-Dufrisne, M. / Wiriyasermkul, P. / Giese, M.H. / Leal-Pinto, E. / Kloss, B. / Tabuso, S. / Love, J. / Punta, M. / Banerjee, S. / ...Authors: Assur Sanghai, Z. / Liu, Q. / Clarke, O.B. / Belcher-Dufrisne, M. / Wiriyasermkul, P. / Giese, M.H. / Leal-Pinto, E. / Kloss, B. / Tabuso, S. / Love, J. / Punta, M. / Banerjee, S. / Rajashankar, K.R. / Rost, B. / Logothetis, D. / Quick, M. / Hendrickson, W.A. / Mancia, F.
History
DepositionApr 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfate transporter CysZ
B: Sulfate transporter CysZ


Theoretical massNumber of molelcules
Total (without water)57,8382
Polymers57,8382
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-33 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.100, 57.020, 96.140
Angle α, β, γ (deg.)90.00, 91.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sulfate transporter CysZ


Mass: 28918.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fragi A22 (bacteria) / Gene: cysZ, AV641_18770
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0X8F058

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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: 4.15 Å3/Da / Density % sol: 70.37 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 6 / Details: PEG400, MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. obs: 20742 / % possible obs: 99.8 % / Redundancy: 27.2 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 12.3
Reflection shellResolution: 3.5→3.6 Å / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.501→39.599 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 40.33 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3437 1055 5.09 %
Rwork0.2939 --
obs0.2964 20742 90.13 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.501→39.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 0 0 3420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053526
X-RAY DIFFRACTIONf_angle_d1.1164814
X-RAY DIFFRACTIONf_dihedral_angle_d14.5141239
X-RAY DIFFRACTIONf_chiral_restr0.071560
X-RAY DIFFRACTIONf_plane_restr0.005580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5006-3.65990.3312720.31421355X-RAY DIFFRACTION50
3.6599-3.85270.36981180.28632441X-RAY DIFFRACTION88
3.8527-4.09380.31211370.27462687X-RAY DIFFRACTION98
4.0938-4.40950.32241510.23972646X-RAY DIFFRACTION98
4.4095-4.85260.34781330.26292649X-RAY DIFFRACTION96
4.8526-5.55310.34541510.26982680X-RAY DIFFRACTION98
5.5531-6.990.39171450.35052626X-RAY DIFFRACTION96
6.99-39.6020.33431480.30462603X-RAY DIFFRACTION96
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)
17.5965-2.8504-0.87314.1978-1.38224.26390.2420.62-0.0913-1.1245-0.84910.8083-0.516-0.68940.31211.1250.7656-0.23372.3359-0.2782.047621.928423.25722.9168
28.9244-2.0860.91463.2778-0.4453.26070.49431.22150.64430.03540.4887-0.5261-0.00691.8932-0.72250.91370.39650.29152.0201-0.07831.926765.511212.20926.2855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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