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- PDB-9dcg: Crystal Structure of the Thiol:Disulfide Interchange Protein DsbC... -

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Basic information

Entry
Database: PDB / ID: 9dcg
TitleCrystal Structure of the Thiol:Disulfide Interchange Protein DsbC from Vibrio cholerae
ComponentsThiol:disulfide interchange protein
KeywordsOXIDOREDUCTASE / thiol:disulfide interchange protein / thioredoxib fold / CSBID / Structural Genomics / Center for Structural Biology of Infectious Diseases
Function / homology
Function and homology information


periplasmic space / membrane
Similarity search - Function
Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase, DsbC/G / Disulfide bond isomerase protein N-terminal domain / : / Thioredoxin-like domain / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin-like superfamily
Similarity search - Domain/homology
FORMIC ACID / Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsKim, Y. / Maltseva, N. / Shatsman, S. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Thiol:Disulfide Interchange Protein DsbC from Vibrio cholerae
Authors: Kim, Y. / Maltseva, N. / Shatsman, S. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionAug 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein
B: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2098
Polymers31,9592
Non-polymers2506
Water93752
1
A: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1325
Polymers15,9791
Non-polymers1524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0773
Polymers15,9791
Non-polymers982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.499, 43.744, 47.851
Angle α, β, γ (deg.)64.074, 80.794, 79.862
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Thiol:disulfide interchange protein


Mass: 15979.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_2418 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9KPF0
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M Lithium sulfate, 150 mM Cacodylate pH 6.5, 1.0 % v/v 1,2 propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 14253 / % possible obs: 90.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 23.18 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.125 / Rrim(I) all: 0.211 / Net I/σ(I): 14.21
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 2 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 4.08 / Num. unique obs: 567 / CC1/2: 0.612 / Rpim(I) all: 0.125 / Rrim(I) all: 0.211 / % possible all: 74.6

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→37.87 Å / SU ML: 0.2884 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.9984
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2567 741 5.21 %
Rwork0.2145 13473 -
obs0.2167 14214 89.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.73 Å2
Refinement stepCycle: LAST / Resolution: 2.09→37.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 11 52 2265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00142280
X-RAY DIFFRACTIONf_angle_d0.40183091
X-RAY DIFFRACTIONf_chiral_restr0.0387340
X-RAY DIFFRACTIONf_plane_restr0.0036406
X-RAY DIFFRACTIONf_dihedral_angle_d13.0911853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.250.29671210.25762186X-RAY DIFFRACTION73.64
2.25-2.480.33081440.27162550X-RAY DIFFRACTION84.32
2.48-2.840.30511460.25112874X-RAY DIFFRACTION95.54
2.84-3.570.2561560.21492948X-RAY DIFFRACTION98.01
3.57-37.870.21321740.17622915X-RAY DIFFRACTION97.17
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)
11.45778174755-0.08133852901760.3439371622360.3307132037250.03061587823110.4682424997610.08203902499710.2533799354180.0131954734559-0.3053308812590.05612627925870.4124646751210.109197968169-0.2042983508860.2533151827680.100657967857-0.0358460261674-0.1573099503560.5051008093320.2046913183510.36644021544619.754803466225.335672166816.4116564161
23.183382543410.146585645759-0.2245939387361.50456280708-0.2613915696920.770044278382-0.2072611808950.0848500797421-0.133772335967-0.1628839790510.04589764319130.2438881705830.0578178491253-0.0360282376652-0.3022262041280.0627383901362-0.082659757809-0.1175331514330.509556671890.1495512171560.36667242697617.146912132715.224406356318.6195719126
37.507293961621.16751899472-3.043847477710.3304774240790.4516486706816.98046854328-0.4778281778210.629328267957-0.352812568663-0.7395685381550.327146906572-0.6145821090270.05036500632850.535409255027-0.005980694401390.311780938193-0.1440718133320.1293136823780.5649450315170.007745762285380.6748549163225.118888053914.281086541317.0106829887
46.40912548113-1.114867755690.2544020004774.947767471061.708298735861.99393599719-0.6580455761410.214167871487-0.929677765978-0.4116727250480.57443659639-0.07461477382020.1255275949170.02398122839340.03765288154840.412737285801-0.1418308387470.08187099996340.271541739424-0.0320688366910.35751061055818.770102912610.774929820115.6073290697
52.709943334731.114369952510.574425036581.692931625180.1370638575170.872221339287-0.135813513442-0.0003839898779460.29773258452-0.01707017556140.02457476927810.343476080721-0.1118614914690.0544664835184-0.1390703989640.122414189721-0.0913307281534-0.02030473784370.4939959446360.2744618947280.39776836625710.784122029124.57482478420.5741163435
64.517871280631.40730170485-0.3911251594320.740419262430.4767510674971.274675627470.05830895095240.0335376293330.728987699497-0.1455827214320.0754349652620.441918484239-0.206102108484-0.45788977915-0.5672605106170.220525629159-0.111349617697-0.04091877183260.4888480141680.2115016660310.37830163548624.609077059534.502802443615.1850690844
76.210674423971.865113312340.6168281657161.91564936380.05497316988680.1945161935730.197882147338-0.5700594903520.511152528290.15565492903-0.1602905562350.0776397534188-0.101084727326-0.102783613762-0.6527795594720.120131333827-0.1428594590880.02506307013340.547567143780.160131973590.23539634532937.619233274236.179957915417.8371146004
84.569179493291.49725029947-0.6145178331492.500104835270.234700650141.85800762755-0.2221290570110.196442272362-0.836255610665-0.01253294708780.226451145576-0.467812280581-0.005354547142650.5077794546950.1519149691150.116572035651-0.0506792343910.05203079274570.5382499888370.1061054868430.342060629477-3.60764523268-8.880013535564.65548091761
91.860682269670.8094095150110.2203310117472.100995285130.246634209041.38400954227-0.2265861101610.1230749725210.303530230012-0.2551223997120.190734677357-0.0455080116086-0.09998089190470.2555927040840.1149960159110.167422346681-0.0922170997134-0.03695625348830.3634994121960.1056171673620.177602636875-0.720955816734-0.317933611562-2.71002907058
101.601917555770.6488028223730.1662187437270.9620140497520.2196250723930.655751580611-0.186377268879-0.0008416157364710.331275130167-0.121267039872-0.01924576994170.313307329735-0.139619131796-0.24341985659-0.068840066950.126489292906-0.0588549973013-0.1601590905050.3892115490970.133619361940.360569814378-9.190023490773.557620353790.321790382397
113.965768812290.218707966289-0.5856744203460.668062192820.08646683423740.3200556046130.234933748405-0.1448371464750.123696869773-0.0311909457776-0.0262598600368-0.0593340293350.0622687404302-0.08156675398260.197453985960.119023434997-0.1355578158640.04206683245060.3792809331330.1104109319990.125288434715-4.69300656076-4.794778443360.873094573549
120.3115549113470.114793057441-0.1026590045960.132927529628-0.07647052149320.338997019611-0.0524889572350.1746857138310.237689053164-0.128727110662-0.0594525032908-0.120063552434-0.1567458266870.205128403249-0.434081265521-0.194499943537-0.3976616013510.131315747650.7941909974260.2096353333770.2432834056228.696324694135.093458424924.39908336356
137.853691234910.5619683269471.298489812335.09131084279-2.337384379883.28151173896-0.06855203042830.217395001738-0.0355620566658-0.095059256398-0.0188329201667-0.0662419379987-0.0328953502258-0.2887259554210.1374995086440.198115115636-0.1141721469760.05344737452710.6020350104810.02400294063940.458632850028-0.9877951926246.253272159157.95614563542
142.546009884120.7682194147241.043125557694.387941235871.798470072752.65491467876-0.125541703435-0.629949217827-0.08173105516940.399474832035-0.1496788014270.306129103895-0.03750151396840.06609045621280.1759432989290.21159016716-0.0843879198818-0.002613481752230.4624135312350.1198614723270.2707899626754.558758277339.442457637610.3095376424
154.31165047551.08574876838-0.3929507920451.626235150020.2117294034731.32584414379-0.1966226254710.417149030044-0.103648740407-0.1667140239060.172995912909-0.1286180119140.03332698446220.14998632325-0.06740888818640.108908903822-0.1156830516870.04299847021460.6212762692580.07916576052820.34822424327213.1601486864-2.512216207240.0250250779171
165.55515214215-0.4240591079660.1591882577387.165267589790.8606902820880.767959184831-0.1965399331960.6021097351840.0708401109972-0.664424806254-0.117459894197-0.492767013421-0.2044913229540.6452780295630.05688939848220.26436942812-0.0672083428496-0.0376647909060.5001902584520.1660275936780.2419607015671.90645015024-0.751985920518-9.21936739262
174.01751439082-1.909815685781.349665174623.27565713755-1.900710699791.40142726790.2259431631550.549054406194-0.232588642239-0.380069513975-0.241703383515-0.10276286070.2132679109360.57596165458-0.3227277317410.162285061234-0.0526023302324-0.1112722836140.5206867195970.08986973702990.122447939885-5.18395461679-4.34596833414-9.93787240196
188.580345736192.70092294478-1.675082008074.85454810789-0.5743821583792.60499831617-0.3397970817830.664393435397-0.637399170135-0.3855149327110.223532789352-0.2654644275530.25794752169-0.0377257583970.3244375788210.181647635523-0.105596859051-0.01126954882980.5228044147580.1138035488360.256424282309-13.3403666363-6.65420613563-9.45269593268
196.853474839592.164554634232.699165498393.92433509794-0.3279615583852.875863277460.161707750203-0.7527247245090.5198781134640.3279929327840.2373820618120.712792836068-0.363015221831-0.695466313182-0.04953964127760.273945955631-0.005705924153570.04810358428520.4184213426310.09989412329750.20971941184227.94158782525.49204194827.5929202502
203.082777234011.011517288270.6567248626561.764897645720.8336627488251.2337773935-0.1774662206230.294448536313-0.154522328476-0.2248730039810.1304667235880.248309245428-0.03503800489350.03640678609420.1804453871030.206075917129-0.127939103567-0.09815920293630.3973257722630.1341167838720.2677280502425.005731766226.99295763216.4522028813
211.632012043090.3978329724240.5969729720530.5821988678770.2016272266660.680850723119-0.1817058743460.249271925093-0.273250415473-0.06219018883370.0399917088002-0.136040988370.06499753831450.1352981556810.02785184186440.13803765077-0.152477243091-0.001504244291080.5420452502850.1519783413710.3258156793933.958876026522.712345972615.0107201299
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 150 through 165 )BC150 - 16542 - 57
22chain 'B' and (resid 166 through 181 )BC166 - 18158 - 73
33chain 'B' and (resid 182 through 186 )BC182 - 18674 - 78
44chain 'B' and (resid 187 through 200 )BC187 - 20079 - 92
55chain 'B' and (resid 201 through 214 )BC201 - 21493 - 106
66chain 'B' and (resid 215 through 238 )BC215 - 238107 - 130
77chain 'B' and (resid 239 through 250 )BC239 - 250131 - 142
88chain 'A' and (resid 109 through 122 )AA109 - 1221 - 14
99chain 'A' and (resid 123 through 133 )AA123 - 13315 - 25
1010chain 'A' and (resid 134 through 148 )AA134 - 14826 - 40
1111chain 'A' and (resid 149 through 157 )AA149 - 15741 - 49
1212chain 'A' and (resid 158 through 181 )AA158 - 18150 - 73
1313chain 'A' and (resid 182 through 186 )AA182 - 18674 - 78
1414chain 'A' and (resid 187 through 199 )AA187 - 19979 - 91
1515chain 'A' and (resid 200 through 217 )AA200 - 21792 - 109
1616chain 'A' and (resid 218 through 226 )AA218 - 226110 - 118
1717chain 'A' and (resid 227 through 238 )AA227 - 238119 - 130
1818chain 'A' and (resid 239 through 250 )AA239 - 250131 - 142
1919chain 'B' and (resid 109 through 122 )BC109 - 1221 - 14
2020chain 'B' and (resid 123 through 133 )BC123 - 13315 - 25
2121chain 'B' and (resid 134 through 149 )BC134 - 14926 - 41

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