[English] 日本語
Yorodumi
- PDB-5zov: Inward-facing conformation of L-ascorbate transporter UlaA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zov
TitleInward-facing conformation of L-ascorbate transporter UlaA
ComponentsPTS ascorbate-specific subunit IIBC
KeywordsTRANSPORT PROTEIN / L-ascorbate PTS
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Phosphotransferase system component IIBC, sugar-specific, predicted / Phosphotransferase system, sugar-specific permease component / PTS system sugar-specific permease component / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit
Similarity search - Domain/homology
ASCORBIC ACID / : / PTS EIIB type-2 domain-containing protein
Similarity search - Component
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.333 Å
AuthorsWang, J.W.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2015CB910104 China
Ministry of Science and Technology (China)2016YFA0501103 China
National Natural Science Foundation of China31621092 China
CitationJournal: Cell Discov / Year: 2018
Title: Inward-facing conformation of l-ascorbate transporter suggests an elevator mechanism
Authors: Luo, P. / Dai, S. / Zeng, J. / Duan, J. / Shi, H. / Wang, J.
History
DepositionApr 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 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: PTS ascorbate-specific subunit IIBC
B: PTS ascorbate-specific subunit IIBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2496
Polymers101,8172
Non-polymers4324
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-38 kcal/mol
Surface area33970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.336, 107.336, 113.288
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein PTS ascorbate-specific subunit IIBC / UlaA


Mass: 50908.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pasteurella multocida (bacteria) / Gene: AZI96_02610 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: A0A1D7R1K6, UniProt: Q9CMQ1*PLUS
#2: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.28M CaCl2, 0.1M Tris-HCl, pH 7.5,42% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 20489 / % possible obs: 97.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 23
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 2129 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RP9

4rp9


Resolution: 3.333→34.986 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3165 896 4.75 %
Rwork0.2732 --
obs0.2753 18854 88.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.333→34.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6164 0 0 0 6164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026320
X-RAY DIFFRACTIONf_angle_d0.5938586
X-RAY DIFFRACTIONf_dihedral_angle_d11.333596
X-RAY DIFFRACTIONf_chiral_restr0.0381010
X-RAY DIFFRACTIONf_plane_restr0.0031036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3328-3.54140.4113550.31881530X-RAY DIFFRACTION45
3.5414-3.81460.37352010.28753350X-RAY DIFFRACTION100
3.8146-4.19790.32691800.273353X-RAY DIFFRACTION100
4.1979-4.8040.2681710.25283371X-RAY DIFFRACTION100
4.804-6.04740.32841280.28093425X-RAY DIFFRACTION100
6.0474-34.98780.29411610.26842929X-RAY DIFFRACTION87
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)
10.0911-0.028-0.03590.06930.01080.0729-0.1592-0.01110.15740.0138-0.05370.0197-0.0936-0.0711-0.43480.43480.2568-0.28180.016-0.08480.387630.21971.5995-12.1509
20.03720.00470.02390.0110.00340.00890.11070.08190.0199-0.00890.03410.0236-0.0475-0.05590.13730.61010.4439-0.4620.38860.22260.701834.747911.4422-23.4829
30.06160.06150.06710.1635-0.01460.1086-0.17630.10350.187-0.1342-0.18170.0270.0206-0.1347-0.5320.36890.551-0.31820.3798-0.28380.640824.8626-7.7954-32.0154
40.2128-0.1099-0.02420.07990.02190.1399-0.09060.0797-0.023-0.059-0.2711-0.0959-0.06720.0332-0.54080.33630.43480.2390.47320.13190.361747.4595-4.1049-31.6551
50.261-0.09640.030.37580.04440.5688-0.21770.22530.2253-0.043-0.3381-0.0461-0.21320.1746-0.80060.0372-0.0553-0.2167-0.0243-0.05060.060743.1451-1.0432-23.9299
60.00660.007-0.0010.00270.01380.0469-0.10160.0806-0.0363-0.1033-0.0971-0.0981-0.21750.0556-0.0660.62970.5209-0.02580.76280.48990.569446.38040.6165-36.2251
70.0258-0.0036-0.0007-0.0007-0.00220.0017-0.0197-0.00040.03610.02840.0325-0.0205-0.0098-0.01320.00330.53720.2465-0.46880.28780.16890.357331.66995.5835-35.6845
80.0369-0.01340.01730.0170.01370.0504-0.03310.0268-0.0008-0.0271-0.03130.0368-0.018-0.0011-0.13420.30190.1394-0.14970.3014-0.16370.322327.5982-14.2859-47.8493
90.10490.02420.09190.12410.00060.0392-0.1681-0.11690.17910.3222-0.1081-0.0723-0.3373-0.0498-0.3180.45090.1711-0.2114-0.9066-0.4316-0.022543.93716.69319.4843
100.1505-0.03770.09480.10130.05790.1223-0.2399-0.1062-0.01890.0438-0.03790.066-0.08320.0271-0.28860.84670.1560.09660.0250.01350.263246.2151-5.567523.1136
110.02120.0186-0.01680.026-0.0250.0248-0.0407-0.0136-0.0392-0.0248-0.0159-0.02680.00650.0172-0.03580.53410.00330.32110.4506-0.17160.418321.1755-5.08846.0393
120.2162-0.164-0.08350.12860.06690.0704-0.10160.0204-0.08140.13190.02520.02040.0514-0.0407-0.25490.40460.3755-0.19110.0043-0.23670.320840.9374-5.44325.8265
130.0913-0.0014-0.08140.0031-0.00420.0801-0.1037-0.2076-0.06260.0952-0.12660.1071-0.0723-0.2097-0.08390.92190.16320.22840.6505-0.33990.641228.868-5.458920.8344
140.0815-0.0238-0.00770.09570.03720.0168-0.11720.00020.0274-0.0302-0.03840.00610.0062-0.0805-0.08540.88860.2450.08880.4732-0.56270.51936.99247.713221.645
150.13880.0882-0.1730.0557-0.11080.2264-0.1582-0.06270.02160.0381-0.1180.01070.10090.0408-0.07010.83160.0154-0.26980.3757-0.25980.67455.1201-0.051133.717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 97 )
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 176 )
4X-RAY DIFFRACTION4chain 'A' and (resid 177 through 262 )
5X-RAY DIFFRACTION5chain 'A' and (resid 263 through 356 )
6X-RAY DIFFRACTION6chain 'A' and (resid 357 through 404 )
7X-RAY DIFFRACTION7chain 'A' and (resid 405 through 432 )
8X-RAY DIFFRACTION8chain 'A' and (resid 433 through 460 )
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 154 )
10X-RAY DIFFRACTION10chain 'B' and (resid 155 through 229 )
11X-RAY DIFFRACTION11chain 'B' and (resid 230 through 262 )
12X-RAY DIFFRACTION12chain 'B' and (resid 263 through 324 )
13X-RAY DIFFRACTION13chain 'B' and (resid 325 through 405 )
14X-RAY DIFFRACTION14chain 'B' and (resid 406 through 432 )
15X-RAY DIFFRACTION15chain 'B' and (resid 433 through 460 )

+
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://pdbjlvh1.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