[English] 日本語
Yorodumi
- PDB-8i01: Crystal structure of Escherichia coli glyoxylate carboligase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i01
TitleCrystal structure of Escherichia coli glyoxylate carboligase
ComponentsGlyoxylate carboligase
KeywordsLIGASE / GCL
Function / homology
Function and homology information


tartronate-semialdehyde synthase / tartronate-semialdehyde synthase activity / glycolate catabolic process / acetolactate synthase complex / glyoxylate catabolic process / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / FAD binding / flavin adenine dinucleotide binding ...tartronate-semialdehyde synthase / tartronate-semialdehyde synthase activity / glycolate catabolic process / acetolactate synthase complex / glyoxylate catabolic process / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / FAD binding / flavin adenine dinucleotide binding / magnesium ion binding / identical protein binding
Similarity search - Function
: / Glyoxylate carboligase / Thiamine pyrophosphate enzyme / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / THIAMINE DIPHOSPHATE / 2,3-DIMETHOXY-5-METHYL-1,4-BENZOQUINONE / Glyoxylate carboligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKim, J.H. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Engineering of two thiamine diphosphate-dependent enzymes for the regioselective condensation of C1-formaldehyde into C4-erythrulose.
Authors: Kim, J.H. / Cheon, H. / Jo, H.J. / Kim, J.W. / Kim, G.Y. / Seo, H.R. / Seo, P.W. / Kim, J.S. / Park, J.B.
History
DepositionJan 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2024Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_initial_refinement_model
Item: _pdbx_entry_details.has_protein_modification / _pdbx_initial_refinement_model.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glyoxylate carboligase
B: Glyoxylate carboligase
C: Glyoxylate carboligase
D: Glyoxylate carboligase
E: Glyoxylate carboligase
F: Glyoxylate carboligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)398,74440
Polymers389,0506
Non-polymers9,69434
Water46,5692585
1
A: Glyoxylate carboligase
B: Glyoxylate carboligase
hetero molecules

A: Glyoxylate carboligase
B: Glyoxylate carboligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,86228
Polymers259,3664
Non-polymers6,49524
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area32110 Å2
ΔGint-247 kcal/mol
Surface area65970 Å2
MethodPISA
2
C: Glyoxylate carboligase
D: Glyoxylate carboligase
E: Glyoxylate carboligase
F: Glyoxylate carboligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,81326
Polymers259,3664
Non-polymers6,44722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32010 Å2
ΔGint-248 kcal/mol
Surface area65990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.617, 189.617, 248.631
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glyoxylate carboligase / Tartronate-semialdehyde synthase


Mass: 64841.590 Da / Num. of mol.: 6 / Mutation: M488L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: gcl, b0507, JW0495 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0AEP7, tartronate-semialdehyde synthase

-
Non-polymers , 5 types, 2619 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-UQ0 / 2,3-DIMETHOXY-5-METHYL-1,4-BENZOQUINONE


Mass: 182.173 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C9H10O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2585 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10 mM Tris-HCl (pH 8.0), 0.5 M sodium chloride, 40 mM dithiothreitol, 0.5% (v/v) polyethylene glycol 6000 (PEG6K), using hanging-drop vapor-diffusion method

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 243437 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 26.26 Å2 / Rmerge(I) obs: 0.992 / Χ2: 0.085 / Net I/σ(I): 2.5 / Num. measured all: 5204950
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.15-2.199.71.581235220.4151100
2.19-2.239.81.45234860.4251100
2.23-2.279.71.261235590.4711100
2.27-2.329.81.16235890.4551100
2.32-2.379.81.077234630.4691100
2.37-2.429.70.949235660.4891100
2.42-2.489.30.824234810.5171100
2.48-2.559.80.7234590.5561100
2.55-2.6210.80.642235460.5811100
2.62-2.71110.582235380.6051100
2.71-2.8111.10.508234920.6531100
2.81-2.9211.40.432235650.7221100
2.92-3.0511.50.363235180.8241100
3.05-3.21110.305235140.8991100
3.21-3.4111.80.253234990.9981100
3.41-3.6812.90.213235361.0061100
3.68-4.0512.90.184235081.0731100
4.05-4.6312.60.153235721.0461100
4.63-5.8313.20.135234820.9051100
5.83-5013.60.093235810.7461100

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXv2.0refinement
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→48.58 Å / SU ML: 0.2516 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.6745
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2311 9711 4 %
Rwork0.1911 233091 -
obs0.1927 242802 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.86 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27243 0 640 2585 30468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008428461
X-RAY DIFFRACTIONf_angle_d1.025338719
X-RAY DIFFRACTIONf_chiral_restr0.06224320
X-RAY DIFFRACTIONf_plane_restr0.01084996
X-RAY DIFFRACTIONf_dihedral_angle_d15.620510329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.170.32263170.31237590X-RAY DIFFRACTION98.43
2.17-2.20.33253220.30477728X-RAY DIFFRACTION99.96
2.2-2.230.32583190.28987658X-RAY DIFFRACTION99.99
2.23-2.260.30473230.28977753X-RAY DIFFRACTION99.99
2.26-2.290.32373220.27867708X-RAY DIFFRACTION99.89
2.29-2.320.30323210.25837720X-RAY DIFFRACTION99.83
2.32-2.350.30653200.25777673X-RAY DIFFRACTION99.81
2.35-2.380.31163220.25327712X-RAY DIFFRACTION99.91
2.38-2.420.29843230.24427744X-RAY DIFFRACTION99.85
2.42-2.460.27783220.22867733X-RAY DIFFRACTION99.93
2.46-2.50.26353210.21927705X-RAY DIFFRACTION99.81
2.5-2.550.273210.2137689X-RAY DIFFRACTION99.86
2.55-2.60.25283240.20757760X-RAY DIFFRACTION99.83
2.6-2.650.25113220.20657728X-RAY DIFFRACTION99.79
2.65-2.710.21963210.19837743X-RAY DIFFRACTION99.84
2.71-2.770.23813230.19737732X-RAY DIFFRACTION99.86
2.77-2.840.24933220.20087758X-RAY DIFFRACTION99.83
2.84-2.920.25623240.19367754X-RAY DIFFRACTION99.88
2.92-30.22953240.19097769X-RAY DIFFRACTION99.89
3-3.10.24213230.18397755X-RAY DIFFRACTION99.89
3.1-3.210.24153240.18577797X-RAY DIFFRACTION99.84
3.21-3.340.24023250.18277768X-RAY DIFFRACTION99.73
3.34-3.490.2173240.17287787X-RAY DIFFRACTION99.74
3.49-3.680.19573250.16467804X-RAY DIFFRACTION99.72
3.68-3.910.2163260.16157834X-RAY DIFFRACTION99.9
3.91-4.210.18743280.14137864X-RAY DIFFRACTION99.94
4.21-4.630.15843290.13147894X-RAY DIFFRACTION99.85
4.63-5.30.18643280.1477884X-RAY DIFFRACTION99.55
5.3-6.680.20743340.17498001X-RAY DIFFRACTION99.93
6.68-48.580.17423320.16368046X-RAY DIFFRACTION96.42
Refinement TLS params.Method: refined / Origin x: -47.799450529 Å / Origin y: 55.7337415966 Å / Origin z: -110.278491991 Å
111213212223313233
T0.223618579929 Å2-0.0288987816745 Å20.00842846446468 Å2-0.161419230615 Å20.0137663521402 Å2--0.21806707822 Å2
L0.111503165123 °2-0.041858908197 °20.0309794836815 °2-0.0551772365344 °2-0.0294074697348 °2--0.0629474214733 °2
S0.0140644285881 Å °0.0245442207957 Å °-0.00762803139439 Å °-0.0074750514906 Å °-0.00501022707024 Å °-0.0170280717746 Å °0.0043633263679 Å °-0.00176200319819 Å °-0.00739204039735 Å °
Refinement TLS groupSelection details: all

+
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