[English] 日本語
Yorodumi
- PDB-6bxg: 1.45 Angstrom Resolution Crystal Structure of PDZ domain of Carbo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bxg
Title1.45 Angstrom Resolution Crystal Structure of PDZ domain of Carboxy-Terminal Protease from Vibrio cholerae in Complex with Peptide.
Components
  • LEU-ILE-ALA
  • Tail-specific protease
KeywordsHYDROLASE/PEPTIDE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / PDZ domain / HYDROLASE / HYDROLASE-PEPTIDE complex
Function / homology
Function and homology information


serine-type peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / signal transduction / proteolysis
Similarity search - Function
B melanoma antigen-like / B melanoma antigen family / Tail specific protease, C-terminal / C-terminal domain of tail specific protease (DUF3340) / Tail specific protease, N-terminal domain / Tail specific protease N-terminal domain / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 ...B melanoma antigen-like / B melanoma antigen family / Tail specific protease, C-terminal / C-terminal domain of tail specific protease (DUF3340) / Tail specific protease, N-terminal domain / Tail specific protease N-terminal domain / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / ClpP/crotonase-like domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
IODIDE ION / Tail-specific protease
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsMinasov, G. / Shuvalova, L. / Filippova, E.V. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.45 Angstrom Resolution Crystal Structure of PDZ domain of Carboxy-Terminal Protease from Vibrio cholerae in Complex with Peptide.
Authors: Minasov, G. / Shuvalova, L. / Filippova, E.V. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tail-specific protease
B: LEU-ILE-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,51714
Polymers11,1772
Non-polymers1,34012
Water1,51384
1
A: Tail-specific protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,20113
Polymers10,8611
Non-polymers1,34012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LEU-ILE-ALA


  • defined by author
  • 315 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)3151
Polymers3151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.579, 35.579, 118.394
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Tail-specific protease


Mass: 10861.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_1496 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q9KRY7
#2: Protein/peptide LEU-ILE-ALA


Mass: 315.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: peptide belongs to not identified protein from E. coli.
Source: (natural) Escherichia coli (E. coli)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.85 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 9.7 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: PACT (E3) 0.2M Sodium iodide, 20% (w/v) PEG 3350..

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 15127 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.021 / Rrim(I) all: 0.058 / Rsym value: 0.054 / Χ2: 1.715 / Net I/σ(I): 51.2
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 775 / CC1/2: 0.893 / Rpim(I) all: 0.3 / Rrim(I) all: 0.817 / Rsym value: 0.759 / Χ2: 1.003 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→29.82 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.1 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.066 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17758 708 4.7 %RANDOM
Rwork0.1324 ---
obs0.1346 14288 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.45→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms754 0 12 84 850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.019797
X-RAY DIFFRACTIONr_bond_other_d0.0010.02824
X-RAY DIFFRACTIONr_angle_refined_deg1.4142.021081
X-RAY DIFFRACTIONr_angle_other_deg0.80631909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3255107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.5925.35728
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.64715149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.569155
X-RAY DIFFRACTIONr_chiral_restr0.080.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02889
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02136
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_it1.6121.604422
X-RAY DIFFRACTIONr_mcbond_other1.612421
X-RAY DIFFRACTIONr_mcangle_it2.052.419531
X-RAY DIFFRACTIONr_mcangle_other2.04933.416532
X-RAY DIFFRACTIONr_scbond_it2.071.98375
X-RAY DIFFRACTIONr_scbond_other2.071375
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5952.831550
X-RAY DIFFRACTIONr_long_range_B_refined3.902815
X-RAY DIFFRACTIONr_long_range_B_other3.779802
X-RAY DIFFRACTIONr_rigid_bond_restr11.9973797
X-RAY DIFFRACTIONr_sphericity_free28.8457
X-RAY DIFFRACTIONr_sphericity_bonded16.5154828
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 57 -
Rwork0.216 1063 -
obs--99.91 %
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)
11.5772-0.4036-0.40623.8919-0.40491.6054-0.0490.0320.03020.00220.12470.0456-0.067-0.1012-0.07570.01240.00680.00260.05450.00540.0039-12.312717.66417.2874
21.1880.37310.16651.6022-0.62551.4383-0.09320.0042-0.08480.03480.0806-0.0113-0.08450.0480.01260.03970.00320.00480.09150.00210.0095-5.022719.47493.0922
32.7656-1.6944-0.42964.0478-0.42241.7999-0.10040.0988-0.1105-0.050.14210.17480.0427-0.1945-0.04160.0254-0.0273-0.00090.0912-0.00130.0105-13.251315.8866-3.887
41.51081.1302-0.14326.4834-1.24541.3022-0.03550.0020.01070.1330.011-0.0843-0.05830.03260.02440.0146-0.0112-0.00170.0581-0.00550.0022-3.124621.9879-0.509
54.70510.0676-6.34570.0044-0.08948.5594-0.0744-0.1198-0.07070.0029-0.0089-0.01920.0940.15510.08340.08740.017-0.00380.12780.01210.1034-11.84694.320410.1283
610.0922-7.3107-3.02527.88571.62991.09710.06390.1205-0.0561-0.0001-0.05620.1096-0.0151-0.0416-0.00770.0270.00090.00230.0457-0.00130.0351-16.987214.98416.5487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A244 - 272
2X-RAY DIFFRACTION2A273 - 289
3X-RAY DIFFRACTION3A290 - 314
4X-RAY DIFFRACTION4A315 - 336
5X-RAY DIFFRACTION5A337 - 341
6X-RAY DIFFRACTION6B1 - 3

+
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