[English] 日本語
Yorodumi
- PDB-4u4m: Crystal structure of 0.5M urea unfolded YagE, a KDG aldolase prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u4m
TitleCrystal structure of 0.5M urea unfolded YagE, a KDG aldolase protein in complex with Pyruvate
ComponentsYagE
KeywordsSUGAR BINDING PROTEIN / TIM barrel / NAL superfamily / KDGA / Schiff base / catalytic triad / Chemical denaturant / Urea promoted unfolding
Function / homology
Function and homology information


2-dehydro-3-deoxy-D-pentonate aldolase / aldonic acid catabolic process / 2-dehydro-3-deoxy-D-pentonate aldolase activity / 2-dehydro-3-deoxy-D-gluconate aldolase / 2-dehydro-3-deoxy-D-gluconate aldolase activity / identical protein binding / cytosol
Similarity search - Function
Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PYRUVIC ACID / UREA / Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsManoj Kumar, P. / Bhaskar, V. / Manicka, S. / Krishnaswamy, S.
Citation
Journal: To be published
Title: Crystal structure of 0.5M urea unfolded YagE, a KDG aldolase protein in complex with Pyruvate
Authors: Manoj Kumar, P. / Bhaskar, V. / Manicka, S. / Krishnaswamy, S.
#1: Journal: Proteins / Year: 2011
Title: Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis.
Authors: Bhaskar, V. / Kumar, M. / Manicka, S. / Tripathi, S. / Venkatraman, A. / Krishnaswamy, S.
#2: Journal: Proteins / Year: 2008
Title: Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12
Authors: Manicka, S. / Unger, T. / Albeck, S. / Dym, O. / Greenblatt, H.M. / Bourenkov, G. / Lamzin, V. / Krishnaswamy, S. / Sussman, J.L.
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YagE
B: YagE
C: YagE
D: YagE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,05328
Polymers128,4794
Non-polymers1,57324
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15060 Å2
ΔGint-4 kcal/mol
Surface area38260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.400, 155.640, 55.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 12 - 309 / Label seq-ID: 1 - 298

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
YagE


Mass: 32119.775 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: YAGE / Plasmid: pET28A / Details (production host): PET28TEVH/YAGE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P75682*PLUS
#2: Chemical
ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH4N2O
#3: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5 / Details: 15% PEG3350, 200mM MgCl2, 100mM HEPES pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9747 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9747 Å / Relative weight: 1
ReflectionResolution: 3.09→19.88 Å / Num. obs: 23206 / % possible obs: 99.67 % / Redundancy: 10.9 % / Biso Wilson estimate: 33.36 Å2 / Rmerge(I) obs: 0.2197 / Net I/σ(I): 11.88
Reflection shellResolution: 3.09→3.2 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.6216 / Mean I/σ(I) obs: 5.17 / % possible all: 99.69

-
Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V8Z

2v8z


Resolution: 3.09→19.88 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.916 / SU B: 20.441 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.494 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24315 1161 5 %RANDOM
Rwork0.21182 ---
obs0.21349 22044 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.599 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å2-0 Å20 Å2
2--3.27 Å20 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 3.09→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9039 0 100 3 9142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199320
X-RAY DIFFRACTIONr_bond_other_d0.0050.029087
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.97412660
X-RAY DIFFRACTIONr_angle_other_deg1.006320849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58751190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93324.453375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.321151487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0631544
X-RAY DIFFRACTIONr_chiral_restr0.0710.21485
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110557
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022051
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0292.4194786
X-RAY DIFFRACTIONr_mcbond_other1.0282.4154765
X-RAY DIFFRACTIONr_mcangle_it1.7123.6235961
X-RAY DIFFRACTIONr_mcangle_other1.7123.6215952
X-RAY DIFFRACTIONr_scbond_it1.1452.5324534
X-RAY DIFFRACTIONr_scbond_other1.1452.5324534
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9343.7526699
X-RAY DIFFRACTIONr_long_range_B_refined3.08319.4510394
X-RAY DIFFRACTIONr_long_range_B_other3.08319.45110395
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A188210.07
12B188210.07
21A189160.07
22C189160.07
31A187250.08
32D187250.08
41B188390.08
42C188390.08
51B189400.08
52D189400.08
61C187180.08
62D187180.08
LS refinement shellResolution: 3.09→3.168 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 83 -
Rwork0.27 1565 -
obs--99.58 %

+
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