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- PDB-5w6l: Crystal Structure of RRSP, a MARTX Toxin Effector Domain from Vib... -

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Basic information

Entry
Database: PDB / ID: 5w6l
TitleCrystal Structure of RRSP, a MARTX Toxin Effector Domain from Vibrio vulnificus CMCP6
ComponentsRTX repeat-containing cytotoxin
KeywordsTOXIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / RRSP / MARTX Toxin / Effector Domain
Function / homology
Function and homology information


RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / Serine aminopeptidase, S33 / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Serine aminopeptidase, S33 ...RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / Serine aminopeptidase, S33 / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Serine aminopeptidase, S33 / Serralysin-like metalloprotease, C-terminal / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
RTX repeat-containing cytotoxin / RTX repeat-containing cytotoxin
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.45 Å
AuthorsMinasov, G. / Wawrzak, Z. / Biancucci, M. / Shuvalova, L. / Dubrovska, I. / Satchell, K.J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Sci Signal / Year: 2018
Title: The bacterial Ras/Rap1 site-specific endopeptidase RRSP cleaves Ras through an atypical mechanism to disrupt Ras-ERK signaling.
Authors: Biancucci, M. / Minasov, G. / Banerjee, A. / Herrera, A. / Woida, P.J. / Kieffer, M.B. / Bindu, L. / Abreu-Blanco, M. / Anderson, W.F. / Gaponenko, V. / Stephen, A.G. / Holderfield, M. / Satchell, K.J.F.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RTX repeat-containing cytotoxin
B: RTX repeat-containing cytotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0166
Polymers115,6962
Non-polymers3204
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-34 kcal/mol
Surface area44870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)247.103, 247.103, 247.103
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein RTX repeat-containing cytotoxin


Mass: 57848.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: XM78_c20952 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1V8MQR3, UniProt: A0A3B6UEL2*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 5.57 Å3/Da / Density % sol: 77.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 15.6 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: 1.96M Ammonium sulfate, 0.1 MOPS (pH 6.5), 20% (v/v) PEG400; Cryo: 4M Formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2013 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.45→30 Å / Num. obs: 33078 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 101.9 Å2 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.046 / Rsym value: 0.113 / Χ2: 1.41 / Net I/σ(I): 18.4
Reflection shellResolution: 3.45→3.51 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 2 / Num. unique obs: 1638 / CC1/2: 0.81 / Rrim(I) all: 0.382 / Rsym value: 0.866 / Χ2: 1.009 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.45→29.97 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / ESU R: 4.15 / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24913 1562 4.8 %RANDOM
Rwork0.22787 ---
obs0.22888 31064 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 121.529 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.45→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7654 0 17 15 7686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197804
X-RAY DIFFRACTIONr_bond_other_d00.027216
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.9710541
X-RAY DIFFRACTIONr_angle_other_deg3.715316777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.2015985
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.46825.214374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.506151310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.5951540
X-RAY DIFFRACTIONr_chiral_restr0.0630.21176
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028776
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021496
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3327.9353946
X-RAY DIFFRACTIONr_mcbond_other1.3337.9353945
X-RAY DIFFRACTIONr_mcangle_it2.34211.8994929
X-RAY DIFFRACTIONr_mcangle_other2.34211.8994930
X-RAY DIFFRACTIONr_scbond_it1.1448.0523858
X-RAY DIFFRACTIONr_scbond_other1.1438.0523858
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.07612.0335613
X-RAY DIFFRACTIONr_long_range_B_refined4.24496.0098949
X-RAY DIFFRACTIONr_long_range_B_other4.24496.0068949
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.45→3.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 113 -
Rwork0.316 2241 -
obs--98.29 %
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)
16.81081.18141.65742.6556-2.30334.15850.21220.38521.1106-0.1977-0.03260.1767-0.3892-0.1929-0.17960.61240.15540.12970.64120.141.2159-23.85528.52785.754
21.76821.29311.03363.55371.71691.55110.0413-0.09990.20770.1403-0.0630.5116-0.3515-0.1480.02170.31750.03040.15420.07740.04480.9665-0.62237.608104.227
32.82810.5561-0.03522.61960.75041.52410.1254-0.16010.10660.29810.0266-0.1696-0.11360.1961-0.15190.1202-0.0378-0.00780.03840.01380.69921.25621.384102.944
43.6550.616-0.49537.13390.37152.04790.04970.1504-0.2079-0.46160.28040.95240.0259-0.463-0.33020.6787-0.1064-0.03590.29960.02070.305614.682102.652105.682
51.13280.46080.38135.11610.97981.8948-0.25810.0823-0.3356-0.85240.36350.2177-0.4152-0.0806-0.10540.6394-0.12490.0840.0599-0.02480.313825.19975.605101.567
61.59160.58180.38283.68330.39172.20260.0814-0.0999-0.64650.3020.2257-1.00250.15310.426-0.30710.41040.0223-0.06020.1209-0.07930.750642.71664.802118.461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3594 - 3678
2X-RAY DIFFRACTION2A3679 - 3835
3X-RAY DIFFRACTION3A3836 - 4087
4X-RAY DIFFRACTION4B3594 - 3670
5X-RAY DIFFRACTION5B3671 - 3832
6X-RAY DIFFRACTION6B3833 - 4087

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