[English] 日本語
Yorodumi
- PDB-3fgp: 2.05 a Crystal Structure of CysM from Mycobacterium Tuberculosis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fgp
Title2.05 a Crystal Structure of CysM from Mycobacterium Tuberculosis - Open and Closed Conformations
ComponentsCysteine synthase B
KeywordsTRANSFERASE / Cysteine synthase / CysM / Tuberculosis / CysO / O-phosphoserine / Amino-acid biosynthesis / Cysteine biosynthesis / Pyridoxal phosphate
Function / homology
Function and homology information


[CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase / Cysteine synthesis from O-phosphoserine / O-phosphoserine sulfhydrylase activity / L-cysteine desulfhydrase activity / cysteine synthase activity / cysteine biosynthetic process / cysteine biosynthetic process from serine / pyridoxal phosphate binding / protein-containing complex / cytosol / cytoplasm
Similarity search - Function
Cysteine synthase / 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
O-phosphoserine sulfhydrylase / O-phosphoserine sulfhydrylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsAgren, D. / Schnell, R. / Schneider, G.
CitationJournal: Febs Lett. / Year: 2009
Title: The C-terminal of CysM from Mycobacterium tuberculosis protects the aminoacrylate intermediate and is involved in sulfur donor selectivity
Authors: Agren, D. / Schnell, R. / Schneider, G.
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine synthase B
B: Cysteine synthase B


Theoretical massNumber of molelcules
Total (without water)69,9042
Polymers69,9042
Non-polymers00
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-19 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.933, 89.142, 99.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cysteine synthase B / CysM / O-acetylserine sulfhydrylase B / CSase B / O-acetylserine (Thiol)-lyase B


Mass: 34952.234 Da / Num. of mol.: 2 / Mutation: T2A
Source method: isolated from a genetically manipulated source
Details: N+terminal His+tag (Removed before crystallization)
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: cysM (Rv1336) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P63873, UniProt: P9WP53*PLUS, O-phosphoserine sulfhydrylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1M Tris-HCl pH 7.5, 0.1M K2HPO4, 4.3M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2008 / Details: torodial focusing mirror
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.05→89.15 Å / Num. all: 41528 / Num. obs: 41528 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 12.2
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2 / Num. unique all: 5922 / Rsym value: 0.554 / % possible all: 97

-
Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DKI

3dki


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.192 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24671 2092 5 %RANDOM
Rwork0.19787 ---
obs0.20041 39379 97.66 %-
all-41528 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.818 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---0.55 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4801 0 0 324 5125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214892
X-RAY DIFFRACTIONr_bond_other_d0.0030.023230
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9756664
X-RAY DIFFRACTIONr_angle_other_deg1.0537835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.825634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81523.077208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.27615748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9581544
X-RAY DIFFRACTIONr_chiral_restr0.0990.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02997
X-RAY DIFFRACTIONr_nbd_refined0.2020.21127
X-RAY DIFFRACTIONr_nbd_other0.2040.23506
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22346
X-RAY DIFFRACTIONr_nbtor_other0.0890.22632
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2311
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0930.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.29
X-RAY DIFFRACTIONr_mcbond_it0.9141.54008
X-RAY DIFFRACTIONr_mcbond_other0.1431.51311
X-RAY DIFFRACTIONr_mcangle_it1.06824983
X-RAY DIFFRACTIONr_scbond_it1.67632032
X-RAY DIFFRACTIONr_scangle_it2.3484.51681
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% reflection obs (%)
2.05-2.1030.2981640.2382815592296.47
2.103-500.2467120920.200413937997.66

+
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