[English] 日本語
Yorodumi
- PDB-4kv3: Ubiquitin-like domain of the Mycobacterium tuberculosis type VII ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kv3
TitleUbiquitin-like domain of the Mycobacterium tuberculosis type VII secretion system protein EccD1 as maltose-binding protein fusion
ComponentsChimera fusion protein of ESX-1 secretion system protein eccD1 and Maltose-binding periplasmic protein
KeywordsPROTEIN TRANSPORT / ESX-1 / ESX / snm4 / ubiquitin / YukD / PF08817 / membrane protein / protein secretion / mbp fusion
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / : / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsKorotkov, K.V. / Evans, T.J.
CitationJournal: Bmc Struct.Biol. / Year: 2016
Title: Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system.
Authors: Wagner, J.M. / Chan, S. / Evans, T.J. / Kahng, S. / Kim, J. / Arbing, M.A. / Eisenberg, D. / Korotkov, K.V.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chimera fusion protein of ESX-1 secretion system protein eccD1 and Maltose-binding periplasmic protein
B: Chimera fusion protein of ESX-1 secretion system protein eccD1 and Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7464
Polymers100,0612
Non-polymers6852
Water7,530418
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-20 kcal/mol
Surface area35710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.680, 125.680, 124.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Chimera fusion protein of ESX-1 secretion system protein eccD1 and Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 50030.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Mycobacterium tuberculosis (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P0AEX9, UniProt: I6X8K0
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES PH 7.5, 1.4M SODIUM CITRATE, vapor diffusion, sitting drop, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 56556 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 44.57 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 17.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.2611.51.0972.88478564161100
2.26-2.323.59469904084100
2.32-2.394.44455543953100
2.39-2.465.03444703853100
2.46-2.546.03427553703100
2.54-2.637.59417043608100
2.63-2.739402693484100
2.73-2.8411.3385943329100
2.84-2.9713.89369303191100
2.97-3.1117.23357143085100
3.11-3.2822338832927100
3.28-3.4826.48319962775100
3.48-3.7231.4298292588100
3.72-4.0235.46278192420100
4.02-4.440255302232100
4.4-4.9243.13231912027100
4.92-5.6842.82203771790100
5.68-6.9644.02171901517100
6.96-9.8451.94131561175100
9.8454.41688565499.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.85 Å
Translation2.5 Å49.85 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ANF

1anf


Resolution: 2.2→49.91 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1982 / WRfactor Rwork: 0.1581 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8806 / SU B: 9.507 / SU ML: 0.127 / SU R Cruickshank DPI: 0.2028 / SU Rfree: 0.1704 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 2862 5.1 %RANDOM
Rwork0.1628 ---
obs0.1649 53741 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.49 Å2 / Biso mean: 42.0955 Å2 / Biso min: 21.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.22 Å20 Å2
2---0.22 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6970 0 46 418 7434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.027180
X-RAY DIFFRACTIONr_bond_other_d0.0010.026832
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9759784
X-RAY DIFFRACTIONr_angle_other_deg0.762315796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46225.676296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.818151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8031518
X-RAY DIFFRACTIONr_chiral_restr0.0720.21110
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021500
X-RAY DIFFRACTIONr_mcbond_it1.4192.4173646
X-RAY DIFFRACTIONr_mcbond_other1.4192.4163645
X-RAY DIFFRACTIONr_mcangle_it2.3473.624554
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 199 -
Rwork0.229 3960 -
all-4159 -
obs--100 %
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)
12.5751-0.1330.92540.4001-0.21571.16730.03310.134-0.1496-0.0754-0.01840.07330.13330.0713-0.01460.10790.0350.00360.08240.01840.061517.24440.98-39.535
23.9010.02642.25590.6682-0.20651.4387-0.1087-0.43820.3607-0.0414-0.0610.05270.0264-0.17610.16970.13810.0863-0.00590.1555-0.00740.131217.43244.83-30.4
33.13470.7054-0.251.8135-0.93111.5302-0.0093-0.12040.23080.28390.05050.2188-0.1559-0.0539-0.04120.1212-0.04750.02740.0812-0.03140.081-14.25158.972-12.374
42.91891.63741.03141.3880.63280.89060.0302-0.075-0.05580.0862-0.04040.00170.162-0.00610.01020.1353-0.0641-0.00980.0839-0.02620.0946-30.40431.886-5.665
52.97771.4771.14782.16580.45890.5114-0.26360.41110.2888-0.19680.20420.162-0.00380.12360.05950.1974-0.1429-0.05030.1758-0.00610.1416-32.36237.099-15.17
63.2038-0.3945-0.23923.2772-0.55830.8410.10650.22810.3697-0.2931-0.2414-0.1037-0.0218-0.0320.13490.12090.0058-0.02920.1470.07220.1065-7.85359.882-33.094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 308
2X-RAY DIFFRACTION2A309 - 369
3X-RAY DIFFRACTION3A373 - 461
4X-RAY DIFFRACTION4B6 - 310
5X-RAY DIFFRACTION5B311 - 371
6X-RAY DIFFRACTION6B372 - 461

+
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