[English] 日本語
Yorodumi
- PDB-1to3: Structure of yiht from Salmonella typhimurium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1to3
TitleStructure of yiht from Salmonella typhimurium
ComponentsPutative aldolase yihT
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta-alpha barrel / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


sulfofructosephosphate aldolase / 6-deoxy-6-sulfofructose-1-phosphate aldolase activity / 6-sulfoquinovose(1-) catabolic process / carbohydrate metabolic process
Similarity search - Function
Sulfofructosephosphate aldolase, YihT / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / PHOSPHATE ION / Sulfofructosephosphate aldolase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsGorman, J. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of yiht from Salmonella typhimurium
Authors: Gorman, J. / Shapiro, L.
History
DepositionJun 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE THE BIOLOGICAL UNIT IS LIKELY A DIMER.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative aldolase yihT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,81713
Polymers33,8131
Non-polymers1,00412
Water2,162120
1
A: Putative aldolase yihT
hetero molecules

A: Putative aldolase yihT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,63426
Polymers67,6262
Non-polymers2,00824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)141.144, 141.144, 102.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

DetailsLikely Dimer: -x+1, -y, z

-
Components

#1: Protein Putative aldolase yihT


Mass: 33813.000 Da / Num. of mol.: 1 / Mutation: A289G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: YIHT, STM4022 / Plasmid: MODIFIED PET26B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9L7R9, Lyases; Carbon-carbon lyases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2% PEG 4000, 0.1M Cacodylate pH 6.5, 1.5M NaKPhosphate pH 8.5, 8% Glycerol; Cryoprotectant - 2% PEG 4000, 0.1M Cacodylate pH 6.5, 1.5M NaKPhosphate pH 8.5, 30% Glycerol, 1M NaBr, pH 7.4, ...Details: 2% PEG 4000, 0.1M Cacodylate pH 6.5, 1.5M NaKPhosphate pH 8.5, 8% Glycerol; Cryoprotectant - 2% PEG 4000, 0.1M Cacodylate pH 6.5, 1.5M NaKPhosphate pH 8.5, 30% Glycerol, 1M NaBr, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 19, 2003 / Details: Vertical and horizontal focusing mirrors
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 14427 / Num. obs: 14427 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 9.4
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 4.14 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.1 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.368 / ESU R Free: 0.238 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20825 721 5 %RANDOM
Rwork0.17867 ---
all0.18018 14392 --
obs0.18018 14392 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.502 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20 Å2
2---1.78 Å20 Å2
3---3.55 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 24 120 2362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222263
X-RAY DIFFRACTIONr_bond_other_d0.0010.022133
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9693057
X-RAY DIFFRACTIONr_angle_other_deg0.83634950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4345289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69224.27196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.56415404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6621518
X-RAY DIFFRACTIONr_chiral_restr0.0760.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02434
X-RAY DIFFRACTIONr_nbd_refined0.2220.2521
X-RAY DIFFRACTIONr_nbd_other0.1950.22262
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.21272
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8311.51733
X-RAY DIFFRACTIONr_mcbond_other0.1191.5592
X-RAY DIFFRACTIONr_mcangle_it0.95622309
X-RAY DIFFRACTIONr_scbond_it1.5263898
X-RAY DIFFRACTIONr_scangle_it2.3194.5748
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.7-2.7690.31400.3189961041
2.769-2.8430.387500.27998
2.843-2.9240.3640.253985
2.924-3.0120.286450.241971
3.012-3.1080.331440.24923
3.108-3.2150.343470.221910
3.215-3.3330.243480.204867
3.333-3.4650.232440.183842
3.465-3.6130.183370.182819
3.614-3.7840.167260.167762
3.784-3.9810.186410.155758
3.981-4.2120.18400.141692
4.212-4.4890.151390.123683
4.489-4.8280.125310.127621
4.828-5.2580.14310.14583
5.258-5.8290.208290.15538
5.829-6.6370.224200.171483
6.637-7.9140.126190.143428
7.914-10.4070.146190.14349
10.407-200.13370.213250

+
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