[English] 日本語
Yorodumi
- PDB-1zud: Structure of ThiS-ThiF protein complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zud
TitleStructure of ThiS-ThiF protein complex
Components
  • Adenylyltransferase thiF
  • ThiS protein
KeywordsTRANSFERASE/BIOSYNTHETIC PROTEIN / Thiamin / Thiazole / protein-protein complex / THIS / THIF / TRANSFERASE-BIOSYNTHETIC PROTEIN COMPLEX
Function / homology
Function and homology information


sulfur carrier protein ThiS adenylyltransferase / adenylyltransferase complex / sulfurtransferase complex / thiazole biosynthetic process / sulfur carrier activity / ubiquitin-like modifier activating enzyme activity / AMPylase activity / sulfotransferase activity / thiosulfate sulfurtransferase activity / thiamine diphosphate biosynthetic process ...sulfur carrier protein ThiS adenylyltransferase / adenylyltransferase complex / sulfurtransferase complex / thiazole biosynthetic process / sulfur carrier activity / ubiquitin-like modifier activating enzyme activity / AMPylase activity / sulfotransferase activity / thiosulfate sulfurtransferase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / nucleotidyltransferase activity / nucleotide binding / protein homodimerization activity / zinc ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Thiazole biosynthesis adenylyltransferase ThiF / ThiS, thiamine-biosynthesis / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Beta-grasp domain ...Thiazole biosynthesis adenylyltransferase ThiF / ThiS, thiamine-biosynthesis / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / NAD(P)-binding Rossmann-like Domain / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sulfur carrier protein ThiS / Sulfur carrier protein ThiS adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsEalick, S.E. / Lehmann, C.
CitationJournal: Biochemistry / Year: 2006
Title: Structure of the Escherichia coli ThiS-ThiF Complex, a Key Component of the Sulfur Transfer System in Thiamin Biosynthesis.
Authors: Lehmann, C. / Begley, T.P. / Ealick, S.E.
History
DepositionMay 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Adenylyltransferase thiF
2: ThiS protein
3: Adenylyltransferase thiF
4: ThiS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,87110
Polymers68,6144
Non-polymers2576
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
3: Adenylyltransferase thiF
4: ThiS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4355
Polymers34,3072
Non-polymers1283
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-22 kcal/mol
Surface area14070 Å2
MethodPISA
3
1: Adenylyltransferase thiF
2: ThiS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4355
Polymers34,3072
Non-polymers1283
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-29 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.505, 111.171, 114.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules 1324

#1: Protein Adenylyltransferase thiF


Mass: 26991.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pET22b / Production host: Escherichia coli (E. coli)
References: UniProt: P30138, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein ThiS protein


Mass: 7315.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: O32583

-
Non-polymers , 4 types, 396 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.27 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 35 mM CaCl2, 100 mM TRIS, 7% PEG400, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2005
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→27 Å / Num. obs: 42351 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 19.4 Å2 / Limit h max: 24 / Limit h min: 0 / Limit k max: 54 / Limit k min: 0 / Limit l max: 57 / Limit l min: 0 / Observed criterion F max: 741150.44 / Observed criterion F min: 0.55 / Rsym value: 0.089 / Net I/σ(I): 21.1
Reflection shellResolution: 1.98→2.05 Å / % possible all: 93.6

-
Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT1.601data extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JW9

1jw9


Resolution: 1.98→24.23 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2080 5 %RANDOM
Rwork0.174 ---
all-44703 --
obs-41515 92.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 72.9701 Å2 / ksol: 0.413118 e/Å3
Displacement parametersBiso max: 96.32 Å2 / Biso mean: 33.74 Å2 / Biso min: 6.79 Å2
Baniso -1Baniso -2Baniso -3
1--4.92 Å20 Å20 Å2
2--12.04 Å20 Å2
3----7.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.17 Å
Luzzati d res low-25 Å
Luzzati sigma a0.11 Å0.07 Å
Luzzati d res high-1.98
Refinement stepCycle: LAST / Resolution: 1.98→24.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 0 6 390 4966
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_torsion_deg24.8
X-RAY DIFFRACTIONc_torsion_impr_deg1.16
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.98-2.070.242224.60.19846090.0165535483187.3
2.07-2.180.2512464.70.18250090.0165493525595.6
2.18-2.320.2332765.20.1850460.0145519532296.4
2.32-2.490.2312654.90.15551410.0145545540697.5
2.49-2.740.2142805.10.15751600.0135560544097.8
2.74-3.140.2012825.10.15651970.0125568547998.4
3.14-3.950.232665.10.16649740.0145645524092.8
3.95-24.230.2432435.40.20442990.0165871454277.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

+
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