[English] 日本語
Yorodumi
- PDB-6vju: Crystal Structure of Cystathionine beta synthase from Legionella ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vju
TitleCrystal Structure of Cystathionine beta synthase from Legionella pneumophila with LLP, PLP, and homocysteine
Components(Cystathionine beta- ...) x 2
KeywordsLYASE / SSGCID / PLP / LLP / synthase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / lyase activity
Similarity search - Function
Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / PYRIDOXAL-5'-PHOSPHATE / Cystathionine beta-lyase / Cystathionine beta synthase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Cystathionine beta synthase from Legionella pneumophila with LLP, PLP, and homocysteine
Authors: Bolejack, M.J. / Davies, D.R. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Apr 3, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cystathionine beta-lyase
B: Cystathionine beta-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,50221
Polymers71,0852
Non-polymers1,41619
Water10,773598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-7 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.350, 91.790, 93.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 30 or resid 32...
21(chain B and (resid 9 through 30 or resid 32...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 9 through 30 or resid 32...A9 - 30
121(chain A and (resid 9 through 30 or resid 32...A32 - 50
131(chain A and (resid 9 through 30 or resid 32...A52 - 63
141(chain A and (resid 9 through 30 or resid 32...A8 - 324
151(chain A and (resid 9 through 30 or resid 32...A0
161(chain A and (resid 9 through 30 or resid 32...A0
171(chain A and (resid 9 through 30 or resid 32...A8 - 324
181(chain A and (resid 9 through 30 or resid 32...A134 - 136
191(chain A and (resid 9 through 30 or resid 32...A8 - 324
1101(chain A and (resid 9 through 30 or resid 32...A150 - 226
1111(chain A and (resid 9 through 30 or resid 32...A293 - 91
1121(chain A and (resid 9 through 30 or resid 32...A293
1131(chain A and (resid 9 through 30 or resid 32...A8 - 324
1141(chain A and (resid 9 through 30 or resid 32...A8 - 324
1151(chain A and (resid 9 through 30 or resid 32...A8 - 324
1161(chain A and (resid 9 through 30 or resid 32...A8 - 324
211(chain B and (resid 9 through 30 or resid 32...B9 - 30
221(chain B and (resid 9 through 30 or resid 32...B32 - 50
231(chain B and (resid 9 through 30 or resid 32...B52 - 63
241(chain B and (resid 9 through 30 or resid 32...B65 - 98
251(chain B and (resid 9 through 30 or resid 32...B100
261(chain B and (resid 9 through 30 or resid 32...B102 - 110
271(chain B and (resid 9 through 30 or resid 32...B112 - 125
281(chain B and (resid 9 through 30 or resid 32...B126 - 128
291(chain B and (resid 9 through 30 or resid 32...B8 - 324
2101(chain B and (resid 9 through 30 or resid 32...B8 - 324
2111(chain B and (resid 9 through 30 or resid 32...B8 - 324
2121(chain B and (resid 9 through 30 or resid 32...B8 - 324

-
Components

-
Cystathionine beta- ... , 2 types, 2 molecules AB

#1: Protein Cystathionine beta-lyase /


Mass: 35656.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_14920, DI056_06925, DI105_06930 / Plasmid: LepnA.01147.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2S6F0T8, UniProt: Q5ZRD1*PLUS
#2: Protein Cystathionine beta-lyase /


Mass: 35428.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_14920, DI056_06925, DI105_06930 / Plasmid: LepnA.01147.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2S6F0T8, UniProt: Q5ZRD1*PLUS

-
Non-polymers , 5 types, 617 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine / Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S
#6: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: LepnA.01147.a.B1.PW38321 was crystallized at 19.49 mg/ml with 4 mM PLP, 4 mM serine, and 4 mM homocysteine and mixed 1:1 with 0.1 M ammonium acetate, 0.1 M Bis-Tris HCl pH 5.5, and 17% (w/v) ...Details: LepnA.01147.a.B1.PW38321 was crystallized at 19.49 mg/ml with 4 mM PLP, 4 mM serine, and 4 mM homocysteine and mixed 1:1 with 0.1 M ammonium acetate, 0.1 M Bis-Tris HCl pH 5.5, and 17% (w/v) PEG 10000. Cryo: 25% EG with 4 mM each ligand. Tray 3295506c1: puck mhb1-1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 25, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.3→41.22 Å / Num. obs: 138423 / % possible obs: 99.7 % / Redundancy: 5.269 % / Biso Wilson estimate: 20.203 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.056 / Χ2: 1.066 / Net I/σ(I): 15.68 / Num. measured all: 729374 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.334.9990.5352.565091910194101860.8930.59999.9
1.33-1.375.2670.4862.9952188991399090.8970.54100
1.37-1.415.2880.4053.5951058966196560.9240.4599.9
1.41-1.455.3040.324.5149490933493300.9520.355100
1.45-1.55.2970.2475.7848132908990860.9720.274100
1.5-1.555.3120.1997.2746687879587890.9780.22199.9
1.55-1.615.3130.168.9645244851885150.9860.177100
1.61-1.685.3230.12711.1643567819181840.9910.14199.9
1.68-1.755.3280.10413.5341710783578280.9930.11599.9
1.75-1.845.3230.08616.440242756675600.9950.09699.9
1.84-1.945.3230.06720.8437924713971250.9960.07499.8
1.94-2.065.2990.05824.5635859677867670.9970.06499.8
2.06-2.25.2670.0527.8433681640263950.9970.05699.9
2.2-2.375.2810.04530.7331465597459580.9980.0599.7
2.37-2.65.2750.04132.9728941550754860.9980.04599.6
2.6-2.915.2830.03835.2126197499849590.9980.04299.2
2.91-3.365.2570.03437.323178445144090.9990.03899.1
3.36-4.115.2470.03239.5119549378537260.9990.03598.4
4.11-5.815.2460.0340.1815219296929010.9990.03397.7
5.81-41.224.9120.02938.618124173616540.9980.03295.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4coo

4coo


Resolution: 1.3→41.22 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1799 1955 1.41 %
Rwork0.1484 136388 -
obs0.1489 138343 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.22 Å2 / Biso mean: 20.8074 Å2 / Biso min: 10.42 Å2
Refinement stepCycle: final / Resolution: 1.3→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 111 598 5519
Biso mean--42.4 32.52 -
Num. residues----634
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2748X-RAY DIFFRACTION5.1TORSIONAL
12B2748X-RAY DIFFRACTION5.1TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.330.24711460.225496549800100
1.33-1.370.24761330.211996449777100
1.37-1.410.25721470.196296619808100
1.41-1.450.26451520.177796689820100
1.45-1.510.17191250.158996969821100
1.51-1.570.16231380.147596739811100
1.57-1.640.19741320.139697549886100
1.64-1.720.17971250.137397179842100
1.72-1.830.19571640.145797039867100
1.83-1.970.16851250.138797679892100
1.97-2.170.1991480.142697779925100
2.17-2.490.17141420.146598259967100
2.49-3.130.16951230.15189860998399
3.13-41.220.15981550.137699891014498

+
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