[English] 日本語
Yorodumi
- PDB-6le3: Crystal structure of gluconate 5-dehydrogenase from Lentibacter a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6le3
TitleCrystal structure of gluconate 5-dehydrogenase from Lentibacter algarum
ComponentsGluconate 5-dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / gluconate 5-dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / Gluconate 5-dehydrogenase
Similarity search - Component
Biological speciesLentibacter algarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYuan, H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of gluconate 5-dehydrogenase from Lentibacter algarum.
Authors: Tian, D. / Fu, X. / Cao, W. / Yuan, H.
History
DepositionNov 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Gluconate 5-dehydrogenase
F: Gluconate 5-dehydrogenase
G: Gluconate 5-dehydrogenase
H: Gluconate 5-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,89513
Polymers108,4984
Non-polymers3969
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14420 Å2
ΔGint-108 kcal/mol
Surface area31430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.424, 55.484, 79.158
Angle α, β, γ (deg.)100.509, 105.662, 97.988
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUPROPRO(chain 'E' and resid 7 through 253)EA7 - 18817 - 198
12PROPROALAALA(chain 'E' and resid 7 through 253)EA192 - 252202 - 262
23LEULEUPROPRO(chain 'F' and (resid 7 through 190 or resid 192 through 253))FB7 - 18817 - 198
24PROPROALAALA(chain 'F' and (resid 7 through 190 or resid 192 through 253))FB192 - 252202 - 262
35LEULEUPROPRO(chain 'G' and (resid 7 through 190 or resid 192 through 253))GC7 - 18817 - 198
36PROPROALAALA(chain 'G' and (resid 7 through 190 or resid 192 through 253))GC192 - 252202 - 262
47LEULEUPROPRO(chain 'H' and (resid 7 through 190 or resid 192 through 253))HD7 - 18817 - 198
48PROPROALAALA(chain 'H' and (resid 7 through 190 or resid 192 through 253))HD192 - 252202 - 262

-
Components

#1: Protein
Gluconate 5-dehydrogenase


Mass: 27124.596 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentibacter algarum (bacteria) / Gene: SAMN05444486_10810 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1H3NGY9
#2: Chemical
ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C2H4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.2 M Ammonium Chloride, 0.1 M Sodium Acetate, pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 49082 / % possible obs: 96.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 26.46 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.07 / Net I/σ(I): 10.34
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.36 / Num. unique obs: 2093 / Rpim(I) all: 0.272 / Rsym value: 0.379

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UF0

3uf0


Resolution: 2.1→37.4 Å / SU ML: 0.2847 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.5419
RfactorNum. reflection% reflection
Rfree0.254 2430 5.08 %
Rwork0.203 --
obs0.2056 47853 93.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.69 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7123 0 27 385 7535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00857266
X-RAY DIFFRACTIONf_angle_d1.12669863
X-RAY DIFFRACTIONf_chiral_restr0.06191142
X-RAY DIFFRACTIONf_plane_restr0.0071307
X-RAY DIFFRACTIONf_dihedral_angle_d8.30124265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.2773960.22145X-RAY DIFFRACTION73.43
2.14-2.190.27621400.23812353X-RAY DIFFRACTION84.91
2.19-2.240.33371550.22522550X-RAY DIFFRACTION90.41
2.24-2.30.29521370.22332680X-RAY DIFFRACTION93.93
2.3-2.360.28711370.21862695X-RAY DIFFRACTION94.91
2.36-2.430.27481530.20672689X-RAY DIFFRACTION93.55
2.43-2.510.28811260.21392650X-RAY DIFFRACTION92.66
2.51-2.60.27211360.22122737X-RAY DIFFRACTION96.67
2.6-2.70.27641440.22362771X-RAY DIFFRACTION97.23
2.7-2.830.30361610.20722740X-RAY DIFFRACTION97.19
2.83-2.970.24551540.22232760X-RAY DIFFRACTION97.43
2.97-3.160.29951620.21722758X-RAY DIFFRACTION96.66
3.16-3.40.26421370.19592746X-RAY DIFFRACTION96.97
3.4-3.750.21551520.18362798X-RAY DIFFRACTION98.14
3.75-4.290.20891500.17692803X-RAY DIFFRACTION98.04
4.29-5.40.20011460.17982758X-RAY DIFFRACTION97.55
5.4-37.40.25781440.21592790X-RAY DIFFRACTION97.57

+
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