[English] 日本語
Yorodumi
- PDB-6arb: CRYSTAL STRUCTURE OF PROTEIN CitE FROM MYCOBACTERIUM TUBERCULOSIS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6arb
TitleCRYSTAL STRUCTURE OF PROTEIN CitE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM, PYRUVATE AND COENZYME A
ComponentsCitrate lyase subunit beta-like protein
KeywordsLYASE / PROTEIN CitE / MYCOBACTERIUM TUBERCULOSIS / COENZYME A / TIM-barrel
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases / oxaloacetate metabolic process / lyase activity / magnesium ion binding
Similarity search - Function
Citrate lyase beta subunit-like / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
COENZYME A / PHOSPHATE ION / PYRUVIC ACID / Citrate lyase subunit beta-like protein / Citrate lyase subunit beta-like protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.717 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wang, H. / Bonanno, J.B. / Carvalho, L. / Almo, S.C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: An essential bifunctional enzyme inMycobacterium tuberculosisfor itaconate dissimilation and leucine catabolism.
Authors: Wang, H. / Fedorov, A.A. / Fedorov, E.V. / Hunt, D.M. / Rodgers, A. / Douglas, H.L. / Garza-Garcia, A. / Bonanno, J.B. / Almo, S.C. / de Carvalho, L.P.S.
#1: Journal: Biorxiv / Year: 2018
Title: Discovery of a novel stereospecific beta-hydroxyacyl-CoA lyase/thioesterase shared by three metabolic pathways in Mycobacterium tuberculosis
Authors: Wang, H. / Fedorov, A.A. / Fedorov, E.V. / Hunt, D.M. / Rodgers, A. / Garza-Garcia, A. / Bonanno, J.B. / Almo, S.C.
History
DepositionAug 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.3Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Mar 1, 2023Group: Database references / Derived calculations / Source and taxonomy
Category: citation / database_2 ...citation / database_2 / entity_src_gen / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _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.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.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.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_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Citrate lyase subunit beta-like protein
B: Citrate lyase subunit beta-like protein
C: Citrate lyase subunit beta-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,24120
Polymers89,8563
Non-polymers3,38517
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15490 Å2
ΔGint-60 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.533, 73.491, 86.459
Angle α, β, γ (deg.)90.00, 99.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

21C-430-

HOH

Detailstrimer by gel filtration

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Citrate lyase subunit beta-like protein


Mass: 29951.939 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: citE, Rv2498c / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P9WPE1, UniProt: P9WPE0*PLUS, Lyases; Carbon-carbon lyases

-
Non-polymers , 6 types, 462 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.4 M Ammonium phosphate, no buffer

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.717→28.454 Å / Num. obs: 163623 / % possible obs: 98.93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 15.6

-
Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
MOSFLMdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U5H

1u5h


Resolution: 1.717→28.454 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 6498 3.97 %
Rwork0.219 --
obs0.2207 163623 98.93 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.315 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6012 Å2-0 Å2-0.8368 Å2
2--0.2971 Å2-0 Å2
3----1.8984 Å2
Refinement stepCycle: LAST / Resolution: 1.717→28.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5976 0 210 445 6631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076274
X-RAY DIFFRACTIONf_angle_d1.0568545
X-RAY DIFFRACTIONf_dihedral_angle_d14.8052302
X-RAY DIFFRACTIONf_chiral_restr0.069975
X-RAY DIFFRACTIONf_plane_restr0.0051119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7173-1.73680.38521720.36184580X-RAY DIFFRACTION87
1.7368-1.75730.37462030.35335145X-RAY DIFFRACTION96
1.7573-1.77870.37612260.325132X-RAY DIFFRACTION98
1.7787-1.80120.33161930.30175340X-RAY DIFFRACTION99
1.8012-1.82490.34371830.32015231X-RAY DIFFRACTION99
1.8249-1.84990.3252050.28835249X-RAY DIFFRACTION99
1.8499-1.87630.37572390.32595282X-RAY DIFFRACTION99
1.8763-1.90430.3322500.27485154X-RAY DIFFRACTION99
1.9043-1.93410.3112250.25545304X-RAY DIFFRACTION99
1.9341-1.96580.27712260.2345243X-RAY DIFFRACTION100
1.9658-1.99970.30972660.23785241X-RAY DIFFRACTION100
1.9997-2.0360.28472230.23365207X-RAY DIFFRACTION100
2.036-2.07520.28631850.23025312X-RAY DIFFRACTION99
2.0752-2.11750.25851930.22155352X-RAY DIFFRACTION100
2.1175-2.16350.25071910.21465385X-RAY DIFFRACTION100
2.1635-2.21390.28472070.21795223X-RAY DIFFRACTION100
2.2139-2.26920.26512040.22515263X-RAY DIFFRACTION100
2.2692-2.33050.28012570.22115242X-RAY DIFFRACTION100
2.3305-2.39910.27662230.20685287X-RAY DIFFRACTION100
2.3991-2.47650.27152190.2015267X-RAY DIFFRACTION100
2.4765-2.56490.25312270.20215253X-RAY DIFFRACTION100
2.5649-2.66750.28212480.20685273X-RAY DIFFRACTION100
2.6675-2.78880.26452480.21255291X-RAY DIFFRACTION100
2.7888-2.93570.27022050.2045307X-RAY DIFFRACTION100
2.9357-3.11950.21162340.20475221X-RAY DIFFRACTION100
3.1195-3.360.25822240.19595318X-RAY DIFFRACTION100
3.36-3.69740.22382180.19085256X-RAY DIFFRACTION100
3.6974-4.2310.21572090.19245260X-RAY DIFFRACTION99
4.231-5.32490.1992100.18995297X-RAY DIFFRACTION100
5.3249-28.45760.26331850.22975210X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6184-0.1783-0.15150.47410.19591.0445-0.02560.0623-0.0875-0.0137-0.02990.07570.1845-0.19230.03520.0744-0.0482-0.00150.09630.00530.0884-13.9019-3.5818-23.0409
20.4198-0.0013-0.09040.919-0.16340.9559-0.01190.0158-0.029-0.1101-0.0267-0.1430.07550.23480.02640.06440.0230.01170.1414-0.00860.099618.98364.7959-22.9733
30.62460.2090.14170.57660.07090.9258-0.08250.04340.1085-0.07960.0410.0807-0.3474-0.12560.02950.11130.0043-0.00790.00620.00690.0528-4.831628.9474-23.1521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

+
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