[English] 日本語
Yorodumi
- PDB-3fzy: Crystal Structure of Pre-cleavage Form of Cysteine Protease Domai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fzy
TitleCrystal Structure of Pre-cleavage Form of Cysteine Protease Domain from Vibrio cholerae RtxA Toxin
ComponentsRTX toxin RtxA
KeywordsTOXIN / RtxA toxin / CPD / Cysteine Protease Domain / Pre-cleavage form / idp00167 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


CoA-dependent peptidyl-lysine N6-palmitoyltransferase activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / host cell cytosol / ligase activity / cysteine-type peptidase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / actin filament organization / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding ...CoA-dependent peptidyl-lysine N6-palmitoyltransferase activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / host cell cytosol / ligase activity / cysteine-type peptidase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / actin filament organization / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
MARTX cysteine protease (CPD) domain / : / C-terminal repeat from RTX toxins / : / Actin cross-linking domain / Actin cross-linking domain / Actin cross-linking (ACD) domain profile. / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain ...MARTX cysteine protease (CPD) domain / : / C-terminal repeat from RTX toxins / : / Actin cross-linking domain / Actin cross-linking domain / Actin cross-linking (ACD) domain profile. / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Multifunctional-autoprocessing repeats-in-toxin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsShuvalova, L. / Minasov, G. / Prochazkova, K. / Satchell, K.J.F. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and molecular mechanism for autoprocessing of MARTX toxin of Vibrio cholerae at multiple sites
Authors: Prochazkova, K. / Shuvalova, L.A. / Minasov, G. / Voburka, Z. / Anderson, W.F. / Satchell, K.J.
History
DepositionJan 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 14, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _struct_ref_seq_dif.details ..._chem_comp.pdbx_synonyms / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RTX toxin RtxA
B: RTX toxin RtxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,45717
Polymers51,1022
Non-polymers1,35615
Water5,639313
1
A: RTX toxin RtxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,24615
Polymers25,5511
Non-polymers69514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RTX toxin RtxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2112
Polymers25,5511
Non-polymers6601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.055, 66.373, 137.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein RTX toxin RtxA


Mass: 25550.953 Da / Num. of mol.: 2 / Fragment: sequence database residues 3440-3650 / Mutation: C3568S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 / Gene: rtxA, VC_1451 / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q9KS12
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: The PEGs II Suite, condition 72 mixed 1:1 v/v with 7.3mg/mL protein, 0.3M NaCl, 0.5mM InsP6, 10mM Tris-HCl (pH 7.4), VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 8.5

-
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: Sep 11, 2008 / Details: beryllium lenses
RadiationMonochromator: single diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. all: 32396 / Num. obs: 32396 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1524 / % possible all: 95.3

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0051refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EEB

3eeb


Resolution: 1.95→23.67 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.849 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Individual Atomic Isotropic Refinement
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.175 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21616 1584 5 %RANDOM
Rwork0.16893 ---
all0.1713 29932 --
obs0.1713 29932 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.053 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å20 Å20 Å2
2---3.42 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.95→23.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 85 313 3672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213635
X-RAY DIFFRACTIONr_bond_other_d0.0010.022328
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9444980
X-RAY DIFFRACTIONr_angle_other_deg0.96635734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5565474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73926.064188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97115599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9791517
X-RAY DIFFRACTIONr_chiral_restr0.0980.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
X-RAY DIFFRACTIONr_mcbond_it1.2591.52259
X-RAY DIFFRACTIONr_mcbond_other0.4071.5931
X-RAY DIFFRACTIONr_mcangle_it2.06223646
X-RAY DIFFRACTIONr_scbond_it3.23731376
X-RAY DIFFRACTIONr_scangle_it4.7734.51334
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 109 -
Rwork0.22 2139 -
obs-2139 98.12 %
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)
13.3935-0.4255-0.93052.97840.6772.00450.09990.36550.2322-0.45770.09830.0997-0.0867-0.1459-0.19820.1146-0.0325-0.05020.06010.05470.06515.739814.397519.1682
24.29421.0321-1.78962.5253-0.28614.64460.0754-0.05140.15220.02810.02160.2279-0.298-0.1343-0.0970.05660.0075-0.03640.01970.0290.116613.952428.58433.151
31.50770.21810.03132.04530.16661.3550.0041-0.00270.0820.07110.11910.0395-0.04130.0239-0.12320.0283-0.0021-0.02040.00860.00640.045120.229117.207332.9826
43.23430.55570.75042.42490.1561.7447-0.136-0.0473-0.02020.04210.1353-0.01330.1538-0.00110.00080.05170.0045-0.0240.00980.00250.028521.35394.727932.7359
51.4937-0.038-0.56662.20290.36680.8126-0.1236-0.0116-0.02520.12710.11390.45630.1269-0.17040.00970.0382-0.0202-0.00480.07730.060.14616.80658.64134.504
61.9998-1.2764-0.74262.33871.07212.93840.09910.11620.6631-0.42560.2045-0.6501-0.52230.3494-0.30360.1669-0.14870.09880.1753-0.02820.26438.40276.09875.4175
73.6211-2.3417-1.58672.42871.52834.27320.39070.56010.6887-0.793-0.1789-0.5489-0.74360.0033-0.21180.393-0.07340.13030.16560.09310.160334.69716.4231-2.3768
83.0781-1.7279-0.443.18680.5882.5612-0.07670.1015-0.0245-0.27650.1388-0.0238-0.1450.0194-0.06210.0634-0.06480.0220.1259-0.04580.018732.2249-6.0075.0134
97.3156-0.2207-1.23554.756-0.2630.9761-0.10260.2956-0.3513-0.47420.03020.1844-0.0635-0.02650.07240.0831-0.06760.01120.1935-0.10020.067231.4256-12.2556-0.667
103.6562-0.4461-0.0914.56661.07191.74810.03830.07150.3895-0.26980.169-0.66740.0150.5496-0.20730.0519-0.04340.09280.2966-0.13880.223548.8732-5.90244.2306
119.1384-0.86882.35799.2878-2.35881.10360.0514-0.03860.03890.46050.10920.7096-0.0937-0.036-0.16060.02390.00520.03610.00390.01370.06757.013918.755438.7037
123.8099-5.8398-1.38389.78221.10751.73990.16780.11510.1593-0.1194-0.1242-0.2541-0.2194-0.0899-0.04350.0694-0.04640.05030.1156-0.04440.059647.4339-2.7661-4.3002
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3419 - 3444
2X-RAY DIFFRACTION2A3445 - 3455
3X-RAY DIFFRACTION3A3456 - 3521
4X-RAY DIFFRACTION4A3522 - 3559
5X-RAY DIFFRACTION5A3560 - 3634
6X-RAY DIFFRACTION6B3424 - 3473
7X-RAY DIFFRACTION7B3474 - 3517
8X-RAY DIFFRACTION8B3518 - 3579
9X-RAY DIFFRACTION9B3580 - 3598
10X-RAY DIFFRACTION10B3599 - 3634
11X-RAY DIFFRACTION11A8000
12X-RAY DIFFRACTION12B8001

+
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