[English] 日本語
Yorodumi
- PDB-5w6l: Crystal Structure of RRSP, a MARTX Toxin Effector Domain from Vib... -

+
Open data


ID or keywords:

Loading...

-
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


Rossmann fold - #11550 / : / Pasteurella multocida toxin, C2 domain / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / CGT/MARTX, cysteine protease (CPD) domain ...Rossmann fold - #11550 / : / Pasteurella multocida toxin, C2 domain / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / Serine aminopeptidase, S33 / 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. / Serralysin-like metalloprotease, C-terminal / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
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
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,1656
Polymers115,8462
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

-
Components

#1: Protein RTX repeat-containing cytotoxin


Mass: 57922.828 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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more