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- PDB-8sfg: Crystal Structure of the Open Unbound Catalytically Inactive Make... -

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Open data


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Basic information

Entry
Database: PDB / ID: 8sfg
TitleCrystal Structure of the Open Unbound Catalytically Inactive Makes Caterpillars Floppy-like (MCF) Effector from Vibrio vulnificus CMCP6
ComponentsAutotransporter adhesin
KeywordsTOXIN / Center for Structural Biology of Infectious Diseases (CSBID) / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / MCF
Function / homology
Function and homology information


host cell cytosol / cysteine-type peptidase activity / transferase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / metal ion binding / membrane
Similarity search - Function
: / C-terminal repeat from RTX toxins / : / : / Pasteurella multocida toxin, C2 domain / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / CGT/MARTX, cysteine protease (CPD) domain ...: / C-terminal repeat from RTX toxins / : / : / Pasteurella multocida toxin, C2 domain / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Serralysin-like metalloprotease, C-terminal / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Autotransporter adhesin
Similarity search - Component
Biological speciesVibrio vulnificus CMCP6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMinasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Herrera, A. / Satchell, K.J.F. / 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)75N93022C00035 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Vibrio MARTX toxin processing and degradation of cellular Rab GTPases by the cytotoxic effector Makes Caterpillars Floppy.
Authors: Herrera, A. / Packer, M.M. / Rosas-Lemus, M. / Minasov, G. / Chen, J. / Brumell, J.H. / Satchell, K.J.F.
History
DepositionApr 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 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
Revision 1.2Sep 24, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autotransporter adhesin
B: Autotransporter adhesin
C: Autotransporter adhesin
D: Autotransporter adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,16444
Polymers160,6554
Non-polymers2,50940
Water1,47782
1
A: Autotransporter adhesin
B: Autotransporter adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,64322
Polymers80,3282
Non-polymers1,31520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
ΔGint-261 kcal/mol
Surface area29100 Å2
MethodPISA
2
C: Autotransporter adhesin
D: Autotransporter adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,52222
Polymers80,3282
Non-polymers1,19420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-230 kcal/mol
Surface area29090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.381, 160.661, 71.793
Angle α, β, γ (deg.)90.000, 101.280, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASPASPAA3219 - 35615 - 347
21GLYGLYASPASPBB3219 - 35615 - 347
12GLUGLUPHEPHEAA3221 - 35607 - 346
22GLUGLUPHEPHECC3221 - 35607 - 346
13GLYGLYASPASPAA3219 - 35615 - 347
23GLYGLYASPASPDD3219 - 35615 - 347
14GLUGLUASPASPBB3221 - 35617 - 347
24GLUGLUASPASPCC3221 - 35617 - 347
15GLYGLYASPASPBB3219 - 35615 - 347
25GLYGLYASPASPDD3219 - 35615 - 347
16GLUGLUPHEPHECC3221 - 35607 - 346
26GLUGLUPHEPHEDD3221 - 35607 - 346

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Autotransporter adhesin


Mass: 40163.848 Da / Num. of mol.: 4 / Mutation: C3351A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus CMCP6 (bacteria) / Gene: VV2_0479 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 / Variant (production host): Magic / References: UniProt: A0A3Q0KY79
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 8.4 mg/ml, 0.5 Sodium chloride, 0.01M Tris pH 8.3; Screen: AmSO4 Suite (B3), 0.2M Cesium sulfate, 2.2M Ammonium sulfate. Cryo: 1.8M Ammonim sulfate, 25% Succrose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 32763 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 54.5 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.059 / Rrim(I) all: 0.125 / Rsym value: 0.11 / Χ2: 1.185 / Net I/σ(I): 13.3
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1579 / CC1/2: 0.627 / CC star: 0.878 / Rpim(I) all: 0.411 / Rrim(I) all: 0.857 / Rsym value: 0.751 / Χ2: 1.002 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.87 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 31.277 / SU ML: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1691 5.2 %RANDOM
Rwork0.1893 ---
obs0.1914 31033 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 180.07 Å2 / Biso mean: 65.041 Å2 / Biso min: 13.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å2-1.64 Å2
2--1.44 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 2.8→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10130 0 128 83 10341
Biso mean--89.86 42.45 -
Num. residues----1313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01310407
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179682
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.63914028
X-RAY DIFFRACTIONr_angle_other_deg0.3241.58722513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.54151306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.52224.004512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.88151738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.131544
X-RAY DIFFRACTIONr_chiral_restr0.0550.21300
X-RAY DIFFRACTIONr_gen_planes_refined0.0530.0211603
X-RAY DIFFRACTIONr_gen_planes_other0.0490.022073
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A96930.1
12B96930.1
21A97240.1
22C97240.1
31A94740.11
32D94740.11
41B95850.12
42C95850.12
51B93510.11
52D93510.11
61C92880.11
62D92880.11
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 125 -
Rwork0.262 2166 -
all-2291 -
obs--93.24 %
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)
110.50964.7194-6.40212.8847-1.52986.4824-0.07660.45510.3084-0.13490.13480.3696-0.0062-0.326-0.05820.25590.0969-0.19490.1374-0.02280.5133-28.12362.20630.05
27.1018-2.25180.2175.6102-1.57269.4282-0.23810.02141.03870.0401-0.1409-0.7403-0.94770.12230.3790.2942-0.066-0.21320.02780.04010.4459-15.35664.32136.23
31.4403-0.19290.33393.12830.41320.9179-0.1505-0.06650.00570.36360.1048-0.25030.062-0.21330.04570.1482-0.0086-0.00590.21190.0030.0405-28.45631.78538.257
40.06210.3476-0.07542.0093-0.46960.12660.1362-0.0294-0.11590.8703-0.1656-0.4981-0.24490.02950.02930.49240.02330.0020.41660.11210.5695-15.6343.92743.598
56.71131.91690.98373.08850.72130.2725-0.00730.1998-0.528-0.37650.0913-0.13120.04170.0191-0.0840.3105-0.05990.04460.0906-0.06820.1652-19.8039.02530.718
64.66-2.9570.9994.78460.654.0989-0.37250.1302-0.5570.150.1809-0.31960.2380.52420.19160.10580.07060.14370.1691-0.0070.3505-2.77918.24839.785
73.3589-0.15221.22082.46491.35254.5972-0.0883-0.1589-0.80480.24250.1908-0.24060.55030.2142-0.10250.24810.09060.18850.04330.07670.394-7.52811.90640.716
84.652-0.35733.23572.10070.3975.58080.1736-0.2341-0.4531-0.1937-0.0722-0.51390.6290.0422-0.10140.2240.067-0.04390.13530.02190.5227-20.512-9.59333.694
93.39781.00630.69747.6274-4.22827.25440.1875-0.3991-1.1380.1879-0.13230.04091.0535-0.0442-0.05520.4129-0.0229-0.09310.09850.07920.6672-31.894-12.30837.036
101.07370.25330.69612.4335-0.17341.29220.0226-0.1145-0.23610.13540.1530.1655-0.0143-0.1583-0.17560.0850.00410.0580.12270.01240.1134-22.27221.36741.459
112.8997-4.41440.07539.22411.96521.8924-0.0744-0.0704-0.0682-0.04010.03810.0597-0.1822-0.05650.03630.1915-0.04730.03130.25980.02030.0531-30.740.04924.679
122.57130.53751.62042.0413-0.38762.0957-0.1620.18790.4992-0.0660.0458-0.1432-0.2327-0.06670.11610.28050.03840.06210.38010.02470.2553-29.17346.03526.849
133.2548-0.2788-1.00975.90712.09585.7004-0.03750.14690.0148-0.0689-0.02650.03630.2861-0.30960.0640.0531-0.06950.0150.25280.02490.0198-39.11130.65924.756
143.90510.7371-1.07732.237-0.55732.9418-0.00260.30120.30550.04140.07680.12830.0366-0.3476-0.07420.11430.01060.00170.2407-0.00350.0299-38.55739.11927.597
159.47312.70860.72545.3660.48220.0795-0.05080.2467-0.46870.53210.02990.29660.03550.04430.02090.2284-0.01040.02680.17150.09910.2109-16.2058.997-0.069
162.24162.94510.80826.37710.28156.14670.18830.2483-0.8581-0.2537-0.0821-0.62881.4675-0.2034-0.10620.60710.03950.02940.2226-0.06880.6669-11.1396.678-9.579
172.3729-0.21390.49163.37970.69941.7886-0.12510.15370.3287-0.3370.1689-0.1144-0.29410.3559-0.04390.1108-0.06470.07620.34310.0070.1748-15.08151.706-12.453
184.6453.0654-1.43635.7243-1.59318.5325-0.1228-0.27210.19810.44490.0644-0.1361-0.0236-0.30150.05840.10370.05310.0050.2829-0.10540.157-1.48253.9042.402
195.4499-0.6955-0.47451.16240.22421.034-0.1589-0.50451.28270.13110.0958-0.1283-0.28030.12820.0630.1316-0.026-0.07110.1417-0.12390.35110.53759.996-2.269
203.73950.8146-1.05212.50240.19683.1311-0.0281-0.10480.4297-0.092-0.07980.0987-0.136-0.15650.10790.00950.011-0.01270.1835-0.00690.08446.92748.438-10.072
218.0329-0.55673.55782.2369-2.14616.0629-0.4451-1.53281.11220.60820.15780.0917-0.7448-0.25770.28730.25350.122-0.08010.4442-0.34310.3785-2.9264.7696.622
225.3207-1.91261.48193.1389-4.12646.2044-0.23420.30160.30560.0118-0.4895-0.17060.08970.74940.72370.2479-0.0910.07550.20840.06310.6542-5.1279.456-3.586
236.398-0.74860.77722.6617-2.69262.73510.36960.01361.45980.8069-0.40920.0553-0.86070.40230.03971.0344-0.14780.23010.2533-0.17211.3487-15.15282.597-7.463
242.8844-0.1165-0.34643.0365-0.74091.1628-0.00080.07020.64510.0794-0.06340.261-0.19990.07260.06420.0473-0.0649-0.02110.2589-0.03760.2357-11.24249.651-11.118
257.16852.3551-1.51086.03-1.28152.28110.0352-0.10990.17520.1081-0.42540.38030.5812-0.06520.39020.38690.01360.08530.37770.02430.2233-25.98632.7590.364
263.4851.076-0.92522.0927-0.48471.8216-0.1266-0.2556-0.52350.0330.0118-0.16890.40990.11220.11480.1349-0.01090.03820.1270.00870.0994-19.69523.952-1.169
273.08340.6540.62622.63790.29952.7772-0.0007-0.0549-0.01740.0967-0.0782-0.14410.1227-0.08530.07890.05240.00890.05490.2056-0.00320.0869-33.50241.251-8.566
283.97680.00091.10591.4468-0.82292.45070.2523-0.4457-0.59990.01950.02460.13270.3227-0.1411-0.27690.2316-0.0130.08060.24840.00820.216-30.3428.091-0.338
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3218 - 3232
2X-RAY DIFFRACTION2A3243 - 3291
3X-RAY DIFFRACTION3A3292 - 3340
4X-RAY DIFFRACTION4A3341 - 3354
5X-RAY DIFFRACTION5A3355 - 3413
6X-RAY DIFFRACTION6A3414 - 3501
7X-RAY DIFFRACTION7A3502 - 3561
8X-RAY DIFFRACTION8B3219 - 3248
9X-RAY DIFFRACTION9B3249 - 3290
10X-RAY DIFFRACTION10B3291 - 3341
11X-RAY DIFFRACTION11B3345 - 3373
12X-RAY DIFFRACTION12B3374 - 3437
13X-RAY DIFFRACTION13B3438 - 3494
14X-RAY DIFFRACTION14B3495 - 3561
15X-RAY DIFFRACTION15C3221 - 3253
16X-RAY DIFFRACTION16C3254 - 3303
17X-RAY DIFFRACTION17C3304 - 3352
18X-RAY DIFFRACTION18C3353 - 3374
19X-RAY DIFFRACTION19C3375 - 3452
20X-RAY DIFFRACTION20C3453 - 3534
21X-RAY DIFFRACTION21C3535 - 3561
22X-RAY DIFFRACTION22D3219 - 3246
23X-RAY DIFFRACTION23D3247 - 3284
24X-RAY DIFFRACTION24D3285 - 3347
25X-RAY DIFFRACTION25D3348 - 3372
26X-RAY DIFFRACTION26D3373 - 3427
27X-RAY DIFFRACTION27D3428 - 3518
28X-RAY DIFFRACTION28D3519 - 3561

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