[English] 日本語
Yorodumi
- PDB-6utn: Native E. coli Glyceraldehyde 3-phosphate dehydrogenase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6utn
TitleNative E. coli Glyceraldehyde 3-phosphate dehydrogenase
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsCYTOSOLIC PROTEIN / G3P / glyceraldehyde 3-phosphate dehydrogenase / E. coli
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
trehalose / ACETATE ION / SN-GLYCEROL-3-PHOSPHATE / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde-3-phosphate dehydrogenase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.79 Å
AuthorsRodriguez-Hernandez, A. / Romo-Arevalo, E. / Rodriguez-Romero, A.
Citation
Journal: Crystals / Year: 2019
Title: A Novel Substrate-Binding Site in the X-Ray Structure of an Oxidized E. coli Glyceraldehyde 3-Phosphate Dehydrogenase Elucidated by Single-Wavelength Anomalous Dispersion
Authors: Rodriguez-Hernandez, A. / Romo-Arevalo, E. / Rodriguez-Romero, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionOct 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: 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_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,72910
Polymers71,6132
Non-polymers1,1168
Water9,836546
1
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,45720
Polymers143,2264
Non-polymers2,23116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area19180 Å2
ΔGint-142 kcal/mol
Surface area44090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.673, 187.353, 121.673
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-707-

HOH

21A-767-

HOH

31A-775-

HOH

41B-725-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

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
11THRTHRGLNGLN(chain 'A' and (resid 1 through 22 or resid 24...AA1 - 211 - 21
12SERSERTYRTYR(chain 'A' and (resid 1 through 22 or resid 24...AA24 - 3924 - 39
13ALAALATYRTYR(chain 'A' and (resid 1 through 22 or resid 24...AA41 - 4241 - 42
14LEULEULYSLYS(chain 'A' and (resid 1 through 22 or resid 24...AA44 - 6944 - 69
15ARGARGVALVAL(chain 'A' and (resid 1 through 22 or resid 24...AA72 - 11772 - 117
16THRTHRPROPRO(chain 'A' and (resid 1 through 22 or resid 24...AA119 - 127119 - 127
17PHEPHELYSLYS(chain 'A' and (resid 1 through 22 or resid 24...AA129 - 159129 - 159
18ILEILELEULEU(chain 'A' and (resid 1 through 22 or resid 24...AA161 - 171161 - 171
19THRTHRGLNGLN(chain 'A' and (resid 1 through 22 or resid 24...AA173 - 182173 - 182
110THRTHRASPASP(chain 'A' and (resid 1 through 22 or resid 24...AA184 - 186184 - 186
111SERSERPROPRO(chain 'A' and (resid 1 through 22 or resid 24...AA189 - 205189 - 205
112THRTHRTHRTHR(chain 'A' and (resid 1 through 22 or resid 24...AA208 - 226208 - 226
113ALAALAGLUGLU(chain 'A' and (resid 1 through 22 or resid 24...AA229 - 247229 - 247
114ALAALAGLYGLY(chain 'A' and (resid 1 through 22 or resid 24...AA249 - 265249 - 265
115LYSLYSGLUGLU(chain 'A' and (resid 1 through 22 or resid 24...AA268 - 286268 - 286
116CYSCYSPHEPHE(chain 'A' and (resid 1 through 22 or resid 24...AA288 - 304288 - 304
117LYSLYSLYSLYS(chain 'A' and (resid 1 through 22 or resid 24...AA306 - 330306 - 330
118HOHHOHHOHHOH(chain 'A' and (resid 1 through 22 or resid 24...AK501
21THRTHRGLNGLN(chain 'B' and (resid 1 through 22 or resid 24...BB1 - 211 - 21
22SERSERTYRTYR(chain 'B' and (resid 1 through 22 or resid 24...BB24 - 3924 - 39
23ALAALATYRTYR(chain 'B' and (resid 1 through 22 or resid 24...BB41 - 4241 - 42
24LEULEULYSLYS(chain 'B' and (resid 1 through 22 or resid 24...BB44 - 6944 - 69
25ARGARGVALVAL(chain 'B' and (resid 1 through 22 or resid 24...BB72 - 11772 - 117
26THRTHRPROPRO(chain 'B' and (resid 1 through 22 or resid 24...BB119 - 127119 - 127
27PHEPHELYSLYS(chain 'B' and (resid 1 through 22 or resid 24...BB129 - 159129 - 159
28ILEILELEULEU(chain 'B' and (resid 1 through 22 or resid 24...BB161 - 171161 - 171
29THRTHRGLNGLN(chain 'B' and (resid 1 through 22 or resid 24...BB173 - 182173 - 182
210THRTHRASPASP(chain 'B' and (resid 1 through 22 or resid 24...BB184 - 186184 - 186
211SERSERPROPRO(chain 'B' and (resid 1 through 22 or resid 24...BB189 - 205189 - 205
212THRTHRTHRTHR(chain 'B' and (resid 1 through 22 or resid 24...BB208 - 226208 - 226
213ALAALAGLUGLU(chain 'B' and (resid 1 through 22 or resid 24...BB229 - 247229 - 247
214ALAALAGLYGLY(chain 'B' and (resid 1 through 22 or resid 24...BB249 - 265249 - 265
215LYSLYSGLUGLU(chain 'B' and (resid 1 through 22 or resid 24...BB268 - 286268 - 286
216CYSCYSPHEPHE(chain 'B' and (resid 1 through 22 or resid 24...BB288 - 304288 - 304
217LYSLYSLYSLYS(chain 'B' and (resid 1 through 22 or resid 24...BB306 - 330306 - 330
218HOHHOHHOHHOH(chain 'B' and (resid 1 through 22 or resid 24...BL501

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase


Mass: 35806.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gapA, ACN002_1253 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0U4BD45, UniProt: P0A9B2*PLUS, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 5 types, 552 molecules

#3: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 5.5 mg/mL protein, 0.1 M HEPES pH 7.5 and 1.43 M sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.79→38.84 Å / Num. obs: 746389 / % possible obs: 99.8 % / Redundancy: 9 % / Biso Wilson estimate: 16.11 Å2 / CC1/2: 0.87 / Net I/σ(I): 37.7
Reflection shellResolution: 1.79→1.82 Å / Num. unique obs: 83268 / CC1/2: 0.87

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→38.84 Å / SU ML: 0.208 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7682
RfactorNum. reflection% reflection
Rfree0.1986 904 1.08 %
Rwork0.178 --
obs0.1782 83405 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.13 Å2
Refinement stepCycle: LAST / Resolution: 1.79→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4925 0 71 546 5542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01515139
X-RAY DIFFRACTIONf_angle_d1.32366998
X-RAY DIFFRACTIONf_chiral_restr0.0852842
X-RAY DIFFRACTIONf_plane_restr0.0085894
X-RAY DIFFRACTIONf_dihedral_angle_d16.84261870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.90.32021480.240413510X-RAY DIFFRACTION98.86
1.9-2.050.22931490.19813638X-RAY DIFFRACTION99.68
2.05-2.260.20671510.185313699X-RAY DIFFRACTION99.91
2.26-2.580.24061490.18313721X-RAY DIFFRACTION99.85
2.58-3.250.20421520.185513780X-RAY DIFFRACTION99.74
3.25-4.860.14681550.150714153X-RAY DIFFRACTION99.78
Refinement TLS params.Method: refined / Origin x: 13.5903451716 Å / Origin y: 62.4994436568 Å / Origin z: 86.5210168461 Å
111213212223313233
T0.0732458179075 Å20.00190388509436 Å20.00214807773928 Å2-0.127043603734 Å20.0122497004732 Å2--0.129704214054 Å2
L0.21072937365 °2-0.0751924035689 °20.140016749036 °2-0.240579278264 °2-0.141409380047 °2--0.918012476066 °2
S0.00698578802943 Å °0.019167498226 Å °0.0188568229492 Å °-0.013621048683 Å °-0.0488825237754 Å °-0.0764764198106 Å °0.00373971959914 Å °0.134079909657 Å °0.0411867259207 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