[English] 日本語
Yorodumi
- PDB-2q3b: 1.8 A Resolution Crystal Structure of O-Acetylserine Sulfhydrylas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q3b
Title1.8 A Resolution Crystal Structure of O-Acetylserine Sulfhydrylase (OASS) Holoenzyme From MYCOBACTERIUM TUBERCULOSIS
ComponentsCysteine synthase A
KeywordsTRANSFERASE / Mycobacterium tuberculosis / Pyridoxal-5'-phosphate / sulphur metabolism / cysteine biosynthesis
Function / homology
Function and homology information


Cysteine synthesis from O-acetylserine / L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process / cysteine biosynthetic process from serine / pyridoxal phosphate binding / extracellular region / cytoplasm / cytosol
Similarity search - Function
Cysteine synthase CysK / 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold ...Cysteine synthase CysK / 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
O-acetylserine sulfhydrylase / O-acetylserine sulfhydrylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchneider, G. / Schnell, R.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural Insights into Catalysis and Inhibition of O-Acetylserine Sulfhydrylase from Mycobacterium tuberculosis: CRYSTAL STRUCTURES OF THE ENZYME {alpha}-AMINOACRYLATE INTERMEDIATE AND AN ...Title: Structural Insights into Catalysis and Inhibition of O-Acetylserine Sulfhydrylase from Mycobacterium tuberculosis: CRYSTAL STRUCTURES OF THE ENZYME {alpha}-AMINOACRYLATE INTERMEDIATE AND AN ENZYME-INHIBITOR COMPLEX.
Authors: Schnell, R. / Oehlmann, W. / Singh, M. / Schneider, G.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 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 A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8046
Polymers33,2961
Non-polymers5085
Water3,657203
1
A: Cysteine synthase A
hetero molecules

A: Cysteine synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,60812
Polymers66,5922
Non-polymers1,01610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7140 Å2
ΔGint-137 kcal/mol
Surface area21910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.991, 70.991, 179.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe OASS forms a dimer, the second part of the biological assembly is generated by the two fold axis: y, x, -z.

-
Components

#1: Protein Cysteine synthase A / O-acetylserine sulfhydrylase A / O-acetylserine Thiol / lyase A / CSase A


Mass: 33296.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: Rv2334 / Gene: cysK / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A534, UniProt: P9WP55*PLUS, cysteine synthase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M HEPES, 80% MPD, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 10, 2006
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→38.46 Å / Num. all: 43621 / Num. obs: 43621 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 3.1 / Num. unique all: 6244 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z7W

1z7w


Resolution: 1.8→37.96 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.844 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.091 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19247 2201 5.1 %RANDOM
Rwork0.17415 ---
all0.17508 41331 --
obs0.17508 41331 99.98 %-
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: 21.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--0.78 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 33 203 2478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222361
X-RAY DIFFRACTIONr_bond_other_d0.0010.022315
X-RAY DIFFRACTIONr_angle_refined_deg1.282.0073224
X-RAY DIFFRACTIONr_angle_other_deg0.82435348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0325315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52923.61794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51815397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2421523
X-RAY DIFFRACTIONr_chiral_restr0.0720.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
X-RAY DIFFRACTIONr_nbd_refined0.210.2490
X-RAY DIFFRACTIONr_nbd_other0.1810.22413
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21188
X-RAY DIFFRACTIONr_nbtor_other0.080.21439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3280.2177
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.213
X-RAY DIFFRACTIONr_mcbond_it0.9411.51964
X-RAY DIFFRACTIONr_mcbond_other0.1551.5621
X-RAY DIFFRACTIONr_mcangle_it1.02322446
X-RAY DIFFRACTIONr_scbond_it1.9333933
X-RAY DIFFRACTIONr_scangle_it2.8914.5770
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 155 -
Rwork0.217 2992 -
obs-2992 100 %

+
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