[English] 日本語
Yorodumi
- PDB-8q57: Crystal structure of class II SFP aldolase from Yersinia aldovae ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q57
TitleCrystal structure of class II SFP aldolase from Yersinia aldovae (YaSqiA-Zn-SO4) with bound sulfate ions
ComponentsTagatose-1,6-bisphosphate aldolase kbaY
KeywordsLYASE / metal-dependent / aldolase / sulfoquinovose / sulfofructose phosphate
Function / homology
Function and homology information


tagatose-bisphosphate aldolase / tagatose-bisphosphate aldolase activity / carbohydrate metabolic process / zinc ion binding
Similarity search - Function
: / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase-type TIM barrel
Similarity search - Domain/homology
Tagatose-1,6-bisphosphate aldolase kbaY
Similarity search - Component
Biological speciesYersinia aldovae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSharma, M. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W003805/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Defining the molecular architecture, metal dependence, and distribution of metal-dependent class II sulfofructose-1-phosphate aldolases.
Authors: Sharma, M. / Kaur, A. / Madiedo Soler, N. / Lingford, J.P. / Epa, R. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J.
History
DepositionAug 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tagatose-1,6-bisphosphate aldolase kbaY
B: Tagatose-1,6-bisphosphate aldolase kbaY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,57215
Polymers67,2532
Non-polymers1,32013
Water4,882271
1
A: Tagatose-1,6-bisphosphate aldolase kbaY
B: Tagatose-1,6-bisphosphate aldolase kbaY
hetero molecules

A: Tagatose-1,6-bisphosphate aldolase kbaY
B: Tagatose-1,6-bisphosphate aldolase kbaY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,14430
Polymers134,5054
Non-polymers2,63926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area12280 Å2
ΔGint-558 kcal/mol
Surface area37630 Å2
Unit cell
Length a, b, c (Å)90.734, 87.525, 104.312
Angle α, β, γ (deg.)90.00, 107.73, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

21B-425-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Tagatose-1,6-bisphosphate aldolase kbaY


Mass: 33626.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia aldovae (bacteria) / Gene: kbaY / Plasmid: pet28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0T9TPS2

-
Non-polymers , 5 types, 284 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: Protein at 16 mg mL-1 in 50 mM NaPi, 300 mM NaCl buffer pH 7.4, using a drop containing 0.6 uL protein and 0.5 uL mother liquor, the latter comprising 1.5 M ammonium sulfate, 0.1 M NaCl, 0.1 M BIS-TRIS pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→61.5 Å / Num. obs: 85319 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Rrim(I) all: 0.079 / Χ2: 1.01 / Net I/σ(I): 12.9 / Num. measured all: 602617
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.181 / Num. measured all: 31344 / Num. unique obs: 4531 / CC1/2: 0.752 / Rpim(I) all: 0.481 / Rrim(I) all: 1.276 / Χ2: 1.06 / Net I/σ(I) obs: 1.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→61.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.23 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20522 4241 5 %RANDOM
Rwork0.18477 ---
obs0.18579 81063 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.012 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å2-0 Å20.06 Å2
2---1.26 Å20 Å2
3---2.14 Å2
Refinement stepCycle: 1 / Resolution: 1.7→61.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 68 271 4520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124355
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164168
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6455900
X-RAY DIFFRACTIONr_angle_other_deg0.521.5689563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.735567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.819523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3210716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02959
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_it2.8462.8282236
X-RAY DIFFRACTIONr_mcbond_other2.8432.8272236
X-RAY DIFFRACTIONr_mcangle_it3.6195.0552792
X-RAY DIFFRACTIONr_mcangle_other3.6185.0562793
X-RAY DIFFRACTIONr_scbond_it3.8923.2122119
X-RAY DIFFRACTIONr_scbond_other3.8913.2142120
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6525.743101
X-RAY DIFFRACTIONr_long_range_B_refined6.85130.54831
X-RAY DIFFRACTIONr_long_range_B_other6.8530.54832
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 308 -
Rwork0.289 5995 -
obs--99.92 %

+
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