[English] 日本語
Yorodumi
- PDB-1wau: Structure of KDPG Aldolase E45N mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wau
TitleStructure of KDPG Aldolase E45N mutant
ComponentsKHG/KDPG ALDOLASE
KeywordsLYASE / KDPG ALDOLASE / ESCHERICHIA COLI / E45N MUTANT / MULTIFUNCTIONAL ENZYME
Function / homology
Function and homology information


(4S)-4-hydroxy-2-oxoglutarate aldolase / 4-hydroxy-2-oxoglutarate aldolase / (4S)-4-hydroxy-2-oxoglutarate aldolase activity / Entner-Doudoroff pathway through 6-phosphogluconate / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / oxaloacetate decarboxylase / 2-dehydro-3-deoxy-phosphogluconate aldolase / oxo-acid-lyase activity / metabolic process / 2-dehydro-3-deoxy-phosphogluconate aldolase activity ...(4S)-4-hydroxy-2-oxoglutarate aldolase / 4-hydroxy-2-oxoglutarate aldolase / (4S)-4-hydroxy-2-oxoglutarate aldolase activity / Entner-Doudoroff pathway through 6-phosphogluconate / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / oxaloacetate decarboxylase / 2-dehydro-3-deoxy-phosphogluconate aldolase / oxo-acid-lyase activity / metabolic process / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / oxaloacetate decarboxylase activity / aldehyde-lyase activity / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
KDPG/KHG aldolase, active site 2 / KDPG and KHG aldolases Schiff-base forming residue. / KDPG/KHG aldolase, active site 1 / KDPG and KHG aldolases active site. / KDPG/KHG aldolase / KDPG and KHG aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
KHG/KDPG aldolase / KHG/KDPG aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMerkel, A.B. / Naismith, J.H.
CitationJournal: Bioorg.Med.Chem. / Year: 2006
Title: Mechanism of the Class I Kdpg Aldolase.
Authors: Fullerton, S.W.B. / Griffiths, J.S. / Merkel, A.B. / Cheriyan, M. / Wymer, N.J. / Hutchins, M.J. / Fierke, C.A. / Toone, E.J. / Naismith, J.H.
History
DepositionOct 28, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KHG/KDPG ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3862
Polymers22,2901
Non-polymers961
Water1,838102
1
A: KHG/KDPG ALDOLASE
hetero molecules

A: KHG/KDPG ALDOLASE
hetero molecules

A: KHG/KDPG ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1586
Polymers66,8703
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.195, 105.195, 51.444
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-2040-

HOH

21A-2058-

HOH

-
Components

#1: Protein KHG/KDPG ALDOLASE / 4-HYDROXY-2-OXOGLUTARATE ALDOLASE / 2-KETO-4-HYDROXYGLUTARATE ALDOLASE / KHG-ALDOLASE / 2-DEHYDRO-3- ...4-HYDROXY-2-OXOGLUTARATE ALDOLASE / 2-KETO-4-HYDROXYGLUTARATE ALDOLASE / KHG-ALDOLASE / 2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE / PHOSPHO-2-DEHYDRO-3-DEOXYGLUCONATE ALDOLASE / PHOSPHO-2-KETO-3-DEOXYGLUCONATE ALDOLASE / 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE


Mass: 22289.941 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET30B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P10177, UniProt: P0A955*PLUS, 2-dehydro-3-deoxy-phosphogluconate aldolase, 4-hydroxy-2-oxoglutarate aldolase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE GLU 45 ASN, CHAIN A

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65 %
Crystal growpH: 8
Details: 0.1M AMMONIUM SULPHATE, 15% PEG4000, 10MM TRIS, PH8.0, pH 8.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→45.55 Å / Num. obs: 15069 / % possible obs: 96.1 % / Observed criterion σ(I): 1.5 / Redundancy: 1.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.5
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.6 / % possible all: 93.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0007refinement
d*TREKdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EUA

1eua


Resolution: 2.8→91.29 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.917 / SU B: 25.119 / SU ML: 0.274 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.595 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 380 4.6 %RANDOM
Rwork0.171 ---
obs0.174 7816 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20.78 Å20 Å2
2--1.56 Å20 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 2.8→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1565 0 5 102 1672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0221597
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3111.9992175
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9035212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.27124.70651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.70915265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.093157
X-RAY DIFFRACTIONr_chiral_restr0.1360.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021167
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3030.2904
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.21114
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3590.2119
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5690.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4410.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0011.51092
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71321702
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8973578
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7434.5473
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.459 23
Rwork0.32 569
Refinement TLS params.Method: refined / Origin x: -36.0048 Å / Origin y: -19.3135 Å / Origin z: 9.4543 Å
111213212223313233
T-0.0725 Å20.0261 Å20.0059 Å2--0.0848 Å20.0134 Å2---0.0887 Å2
L0.8646 °20.7431 °2-0.1001 °2-1.302 °20.2246 °2--0.7354 °2
S-0.0153 Å °0.0373 Å °-0.0576 Å °-0.0565 Å °0.0432 Å °-0.1462 Å °-0.0389 Å °0.0177 Å °-0.028 Å °

+
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