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- PDB-6d9z: Structure of CysZ, a sulfate permease from Pseudomonas Denitrificans -

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Basic information

Entry
Database: PDB / ID: 6d9z
TitleStructure of CysZ, a sulfate permease from Pseudomonas Denitrificans
ComponentsSulfate transporter CysZ
KeywordsTRANSPORT PROTEIN / Membrane protein / sulfate translocation / prokaryotic cysteine biosynthesis
Function / homologySulfate transporter CysZ / Etoposide-induced protein 2.4 (EI24) / sulfate transmembrane transporter activity / sulfate assimilation / cysteine biosynthetic process / plasma membrane => GO:0005886 / Sulfate transporter CysZ
Function and homology information
Biological speciesPseudomonas denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.40213179468 Å
AuthorsSanghai, Z.A. / Clarke, O.B. / Liu, Q. / 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 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 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
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Sulfate transporter CysZ
A: Sulfate transporter CysZ
B: Sulfate transporter CysZ
C: Sulfate transporter CysZ
D: Sulfate transporter CysZ
E: Sulfate transporter CysZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,24726
Polymers166,4006
Non-polymers5,84720
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21350 Å2
ΔGint-91 kcal/mol
Surface area70820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.130, 225.130, 96.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 3 - 238 / Label seq-ID: 3 - 238

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain 'A' and (resid 3 through 60 or (resid 61...AB
2(chain 'B' and (resid 3 through 60 or (resid 61...BC
3(chain 'C' and (resid 3 through 60 or (resid 61...CD
4(chain 'D' and (resid 3 through 114 or (resid 115...DE
5(chain 'E' and (resid 3 through 60 or (resid 61...EF
6(chain 'F' and (resid 3 through 60 or (resid 61...FA

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Components

#1: Protein
Sulfate transporter CysZ


Mass: 27733.320 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas denitrificans (nomen rejiciendum) (bacteria)
Gene: cysZ
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: M4XKU7
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 4.33 Å3/Da / Density % sol: 71.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 22-30% PEG550MME, 0.1 M Na-Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→86 Å / Num. obs: 37223 / % possible obs: 100 % / Redundancy: 19.7 % / Biso Wilson estimate: 171.607658049 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 22.4
Reflection shellResolution: 3.402→3.523 Å / Rmerge(I) obs: 2.89 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3708 / % possible all: 96.87

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Processing

Software
NameVersionClassification
phenix.refine1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Cootmodel building
PHASERphasing
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D79

6d79


Resolution: 3.40213179468→19.9957631618 Å / SU ML: 0.555965948211 / Cross valid method: THROUGHOUT / σ(F): 1.33018353199 / Phase error: 35.528327687
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.288702881638 1937 5.20391166514 %
Rwork0.244775522503 35285 -
obs0.247196502171 37222 96.9802766994 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 195.946588017 Å2
Refinement stepCycle: LAST / Resolution: 3.40213179468→19.9957631618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11415 0 400 0 11815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099000090445212184
X-RAY DIFFRACTIONf_angle_d1.097244511316607
X-RAY DIFFRACTIONf_chiral_restr0.07325291263251945
X-RAY DIFFRACTIONf_plane_restr0.007260910750461949
X-RAY DIFFRACTIONf_dihedral_angle_d12.02217502796866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4021-3.48680.4125761172951370.3712741062212481X-RAY DIFFRACTION96.3562753036
3.4868-3.58050.3258121652131190.3223110883052555X-RAY DIFFRACTION98.0564723139
3.5805-3.68530.3159997343511470.3139117189762517X-RAY DIFFRACTION98.2300884956
3.6853-3.80340.355395232891150.31795341662550X-RAY DIFFRACTION98.3757844223
3.8034-3.93840.3430093705321160.306647835292566X-RAY DIFFRACTION97.8118161926
3.9384-4.09480.375797103531190.312903174432553X-RAY DIFFRACTION97.8754578755
4.0948-4.27940.3419190626941550.2885524854432494X-RAY DIFFRACTION97.5690607735
4.2794-4.50260.3081452552371420.2710334097872534X-RAY DIFFRACTION97.1324863884
4.5026-4.78110.2637485638381420.2578745703222508X-RAY DIFFRACTION96.7859751644
4.7811-5.14440.333719062981660.245663010412455X-RAY DIFFRACTION96.3957337256
5.1444-5.65150.3143273578891290.2769904228412556X-RAY DIFFRACTION97.0715835141
5.6515-6.44520.3289428489491310.2885925789442524X-RAY DIFFRACTION95.9522949042
6.4452-8.03170.2842644461931610.2588618710652482X-RAY DIFFRACTION95.8303118202
8.0317-19.99610.2411263504631580.1775563419622510X-RAY DIFFRACTION94.4424778761
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)
10.712491446509-0.7196231846750.2451762244180.981496785766-0.6124930399520.1418058885680.653319371894-0.757829194021-1.73860352160.490054516821-0.23124365858-1.334672205280.1740677070210.835894824709-0.001833766415911.94731755510.279022082464-0.5281830437792.12451697241-0.2184324942082.2844555086276.603585207658.393747776728.119270337
26.321706456630.737325922181-1.522994515031.662265833350.612270567146-0.0603394540659-0.2601445345760.6142187294850.8907899724390.5930060177050.323515794259-0.46109434968-0.216224788071-0.644668858007-0.0002417175234251.762557247170.184756318643-0.02597000411651.54869316112-0.03094134177891.4542717964748.044952532967.771101100318.0994285755
33.2261592482-1.001760790581.99795812473.04459368750.1813856203634.07374553820.455942983229-0.3394125391760.5919765335070.3675569261760.308885098248-1.07799574421-0.20454478320.5964429094220.000598482651171.715820175510.199584875158-0.1674833777371.55115067634-0.2248057253682.0487031814670.29635595770.786695737819.0191779898
42.04249064536-0.00960350732222-1.662591638020.553239956810.2314360268220.60536902004-0.9573276520971.302935793440.671327170677-0.98892049206-0.5133717880140.376288772601-0.9766039678720.424543560226-0.004328960362712.212944915910.33729768808-0.4272572200991.90275627556-0.2533719998171.5048660092531.964722783753.586957976823.1928599725
51.090109255080.3506898221781.136180247570.9307562195522.163537756170.8489480339280.603415223301-0.341365690953-0.5672028431330.0511491585274-0.349876923118-0.549633244887-0.3582426526190.765034400587-0.0004938552130362.274454528050.0683344719547-0.3860330838721.81105466892-0.02624220418271.6723504561967.821353459744.129032504822.0297569269
62.92161793493-1.773657147732.334853411782.81591562182.419000404411.01414619944-0.204507345052-0.274457258521-0.8132706661460.2414617561270.6904871600280.7637881514960.6111965356620.996146637638-0.0008588192653941.870841068830.352224873818-0.5251407972441.73466754640.1422878882281.5192436743157.172037908743.486587145219.4452859997
73.798248182530.5980296649581.636972913391.53692616118-4.544835885242.153912495250.419070600546-1.00364170514-1.70419812856-0.206970738442-0.9545838377750.4947245548390.6070756433731.17749822537-0.000687225892812.099251452350.146394456159-0.06410678430081.682462344960.1799660942051.9551870638243.346234207937.825618969622.6682464104
8-0.7965626073191.01673464104-1.723918255561.531634391541.50409587283-0.02964389660421.08702294720.6186215633230.138151199992-0.0805657865782-0.05262247300770.1186297443691.06436713569-0.303129946056-0.000869736687342.348512620060.395723718231-0.1134248465652.07186731684-0.08809524308191.6362412998543.141162236840.83191374018.46834400306
92.18084088375-1.40907830717-1.149649224942.1312509745-1.556612271192.651060147440.05406249072680.858054378199-1.04364045382-0.07139949518320.4721348146130.6478665382390.321173067566-0.696805331869-3.76697181416E-51.901837706420.1370967652360.005843296488791.75508910483-0.1016567102732.1228313160735.448091208843.548767195615.9291405799
100.078360319858-0.07238455987830.4993640680350.0313854048044-0.1162993363230.0796574675955-1.936560241430.3571919381761.072209767341.63032504212.56438397456-1.511638692151.9510631285-1.64150829399-0.001150268052123.415045944320.112503318211.267752545541.71267087777-0.07100594026163.0652022555991.015916420651.885728331-33.5621900943
11-0.190126783881-0.258935272307-0.5536040833742.893177506581.684531346280.882816897514-0.0505840129386-0.0258386558034-1.29653249477-0.309128086804-0.9276069999240.380407784562-0.4165179420520.321367116603-0.0002399259089652.485551572010.718494659813-0.5746920483241.89442997233-0.4379974790742.0494788378383.617580079530.4703780587-9.88569394427
124.71777394156-1.964864363723.638279177661.86366817437-0.283523208432.66275366705-0.3633451658191.58607256488-0.3593772980130.433543361764-0.434651285664-1.320684210150.496849600376-0.7469314185170.0004256107338791.932929599250.493036994934-0.220094556171.15024884255-0.2542708939962.1536909993781.757866244238.9684431577-6.45183446525
130.2205452837830.0812121598285-1.121621523083.030815201190.552754147270.218376309583-0.4605413180570.851436340483-1.014739425080.04854685413160.037091992755-1.6924723697-1.092054110210.6938058478030.0004071285338171.820894445920.117865801906-0.3550732302092.2439980948-0.4378522774023.5966057116790.239985414652.1679992237-12.9154931953
141.247080094630.463061044339-2.08934418541.45472703229-2.243441757992.02786526008-1.110166707612.206976097630.4049231270110.2005176213111.28408559352-2.60930160183-0.7489082876150.3498075045290.0002651454353311.6987805025-0.03829128795850.09460096078272.27275209629-0.06508485259283.9726069780491.773547460757.2436730351-21.2171461192
15-0.23316247520.2373839542330.1049104516521.089891805160.234268201980.5587794403790.416623101311-2.452048699281.926215667170.27116454159-0.590407137943-1.85693595506-0.946961043193-0.0508202510840.0008573150141252.17867592196-0.1084102871630.1478529411632.399538397930.08587810422651.7358541729568.840165340617.6049213345-10.928252951
163.6160170446-0.515949816343-0.4130739902960.6136149009050.7129838525170.983892467598-0.1417845360890.863603981061.55247881528-1.21169054234-0.353334350618-2.67652174565-0.598582734812-0.2316207681580.0003811935848782.276727538650.2375191497170.3403793810252.04131814910.394330184092.0348981199574.389017735645.0021868053-34.8334780957
171.567349970091.37532184802-0.4907556177821.108695079551.35804429454-0.26124731802-0.1062220715340.1869529525480.115986715237-0.3287327213630.0687194061946-0.378176130334-0.369809438882-0.474093970270.0001773627396992.171119688940.2792098622110.187706154141.67468064388-0.03281125975361.3544151759969.61639135133.1190363329-28.1123534104
180.922544127201-1.568698739061.401063967017.209828613610.206641838060.7512795969130.1371845565040.1625825910710.0319325793775-0.178007178179-0.09865188413480.329742988012-0.220171566621-0.502605976438-0.0001987058418712.037176124430.1600852033960.0229425045251.72996870249-0.01015752861391.5068817409258.320698580626.7670501756-22.1420762031
190.2081297465750.132168078741-0.7398440508830.1016933623770.1915549315860.427336216431-0.8109115244961.56903558232-0.3377726485122.114362635170.306954035304-0.721048143241-0.229814831575-1.33058218295-0.000953153741222.864011915770.309642405267-0.3753328457892.54292809592-0.4492832904711.5794779848833.805357658160.7044491239-41.6905353262
200.645455274646-0.3811376827820.1504548404994.036918369930.08706390482771.4974538463-0.2249935900460.140788361769-0.241546760391-0.3085975123310.0573938544610.636888803358-1.415499126690.4648535956080.001002848314141.552292431470.193286707730.1222908131841.996800944090.2197096407331.8788865887734.830585100576.9767968352-13.9479344628
212.72966450589-2.24602338668-3.30091032219-0.5698265971071.587780513453.17309227404-0.768829820320.42274165024-0.67107016515-0.04742375140260.05995925316540.08132790497990.4066405177040.399811510531-0.0004525744917072.12326933710.26517741054-0.2702945887741.936518924990.0665027255312.3653787227627.638035097660.9908369423-22.8090906646
221.23105910777-1.59792156143-0.4078655395661.7394362573.799053786114.63715289606-0.8091386848040.55690226453-2.69977211366-0.4329170002670.8016084203510.510500917789-0.111537276230.4035044365930.0007206560301872.152455842280.354210812554-0.05528805541722.552457999240.3378542779542.3600465405329.737607917656.2235383742-30.4131081072
234.507270345210.6644945892382.806149356426.37496205482-0.571923793958-1.905275149160.2081999027060.4328481775460.0360570523658-0.623323365349-0.0242743377165-0.1479352693290.224617129287-0.0842146913205-5.26296364695E-51.900731600510.103948767740.3083895691411.68346640030.2496922771631.8929199459949.349656219278.0260552893-29.9465909704
241.91018771704-2.74041767517-0.2522728081533.984045280593.728088506222.547838771040.6860404124010.7216843769791.03201863527-1.31259686267-0.266659588073-1.23826949312-0.1758242821670.2154056993110.0002019140909662.051157537910.2562611265380.4666366493471.8752907550.5667215413891.8299498918858.447864153981.9953896505-26.7689853095
251.83193727939-1.336644860990.0773423905323.15465981887-1.537489307520.9460634807310.09852250628880.9253828522110.2555980511750.5099538946050.630236590056-0.2456745765310.02579322324950.3423759272110.0003835582656261.735896811070.07245447385530.06970225414651.838618326140.4533196765642.0805436156759.013993861290.7739820649-16.7394425657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 3 through 26 )
2X-RAY DIFFRACTION2chain 'F' and (resid 27 through 109 )
3X-RAY DIFFRACTION3chain 'F' and (resid 110 through 238 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3 through 24 )
5X-RAY DIFFRACTION5chain 'A' and (resid 25 through 63 )
6X-RAY DIFFRACTION6chain 'A' and (resid 64 through 109 )
7X-RAY DIFFRACTION7chain 'A' and (resid 110 through 153 )
8X-RAY DIFFRACTION8chain 'A' and (resid 154 through 184 )
9X-RAY DIFFRACTION9chain 'A' and (resid 185 through 238 )
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 26 )
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 55 )
12X-RAY DIFFRACTION12chain 'B' and (resid 56 through 109 )
13X-RAY DIFFRACTION13chain 'B' and (resid 110 through 177 )
14X-RAY DIFFRACTION14chain 'B' and (resid 178 through 238 )
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 23 )
16X-RAY DIFFRACTION16chain 'C' and (resid 24 through 63 )
17X-RAY DIFFRACTION17chain 'C' and (resid 64 through 119 )
18X-RAY DIFFRACTION18chain 'C' and (resid 120 through 242 )
19X-RAY DIFFRACTION19chain 'D' and (resid 3 through 24 )
20X-RAY DIFFRACTION20chain 'D' and (resid 25 through 109 )
21X-RAY DIFFRACTION21chain 'D' and (resid 110 through 184 )
22X-RAY DIFFRACTION22chain 'D' and (resid 185 through 238 )
23X-RAY DIFFRACTION23chain 'E' and (resid 3 through 63 )
24X-RAY DIFFRACTION24chain 'E' and (resid 64 through 184 )
25X-RAY DIFFRACTION25chain 'E' and (resid 185 through 242 )

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