[English] 日本語
Yorodumi
- PDB-8gsk: Crystal Structure of S302G single mutant of O-acetyl-L-serine sul... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gsk
TitleCrystal Structure of S302G single mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 2.2 A
ComponentsCysteine synthase
KeywordsTRANSFERASE / single mutant / O-acetyl-L-serine sulfhydrylase / Haemophilus influenzae
Function / homology
Function and homology information


cysteine synthase / cystathionine beta-synthase activity / cysteine synthase activity / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / cytoplasm
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. / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme
Similarity search - Domain/homology
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.271 Å
AuthorsKumar, N. / Mahajan, A.S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5236/MED/29/504/20 India
CitationJournal: To Be Published
Title: S302G Crystal Structure of S302G single mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 2.2 A
Authors: Kumar, N. / Mahajan, A.S.
History
DepositionSep 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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


Theoretical massNumber of molelcules
Total (without water)33,6211
Polymers33,6211
Non-polymers00
Water905
1
A: Cysteine synthase

A: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)67,2432
Polymers67,2432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area4020 Å2
ΔGint-19 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.600, 112.600, 45.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein Cysteine synthase / CSase / O-acetylserine (thiol)-lyase / OAS-TL / O-acetylserine sulfhydrylase


Mass: 33621.438 Da / Num. of mol.: 1 / Mutation: S302G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: cysK, HI_1103 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P45040, cysteine synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 1.3 M Sodium Citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 4, 2014
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.271→42.37 Å / Num. obs: 12952 / % possible obs: 96.02 % / Redundancy: 14.4 % / CC1/2: 0.788 / CC star: 0.939 / Net I/σ(I): 44.88
Reflection shellResolution: 2.271→2.352 Å / Num. unique obs: 18871 / CC1/2: 0.745

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y7L

1y7l


Resolution: 2.271→42.37 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.415 / SU ML: 0.223 / Cross valid method: FREE R-VALUE / ESU R: 0.44 / ESU R Free: 0.268
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2664 625 4.839 %
Rwork0.2225 12291 -
all0.225 --
obs-12916 96.023 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.709 Å2
Baniso -1Baniso -2Baniso -3
1--2.295 Å2-0 Å20 Å2
2---2.295 Å2-0 Å2
3---4.59 Å2
Refinement stepCycle: LAST / Resolution: 2.271→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 0 5 2275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122303
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.6313128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0265308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99122.6694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44115381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3851513
X-RAY DIFFRACTIONr_chiral_restr0.1190.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021694
X-RAY DIFFRACTIONr_nbd_refined0.2290.21046
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21581
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.285
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.190.210
X-RAY DIFFRACTIONr_mcbond_it2.23.2641235
X-RAY DIFFRACTIONr_mcangle_it3.3924.8821542
X-RAY DIFFRACTIONr_scbond_it2.5363.361068
X-RAY DIFFRACTIONr_scangle_it3.7014.9561586
X-RAY DIFFRACTIONr_lrange_it5.93960.8119709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.271-2.330.475360.391924X-RAY DIFFRACTION96.7742
2.33-2.3930.301540.301903X-RAY DIFFRACTION100
2.393-2.4630.411340.256877X-RAY DIFFRACTION99.8904
2.463-2.5380.334440.226873X-RAY DIFFRACTION100
2.538-2.6220.239500.223823X-RAY DIFFRACTION100
2.622-2.7140.357280.238619X-RAY DIFFRACTION75.5841
2.714-2.8160.326300.221788X-RAY DIFFRACTION100
2.816-2.9310.295440.233751X-RAY DIFFRACTION99.8744
2.931-3.0610.308410.21731X-RAY DIFFRACTION100
3.061-3.210.28440.206680X-RAY DIFFRACTION100
3.21-3.3830.255320.213662X-RAY DIFFRACTION100
3.383-3.5880.259340.223495X-RAY DIFFRACTION80.0303
3.588-3.8350.237290.258498X-RAY DIFFRACTION85.1373
3.835-4.1420.239320.213483X-RAY DIFFRACTION88.6403
4.142-4.5360.232140.187519X-RAY DIFFRACTION100
4.536-5.0690.144240.181455X-RAY DIFFRACTION100
5.069-5.8490.28200.203417X-RAY DIFFRACTION100
5.849-7.1540.199130.222352X-RAY DIFFRACTION100
7.154-10.0770.176100.187280X-RAY DIFFRACTION100
10.077-42.370.326120.183161X-RAY DIFFRACTION99.4253

+
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://pdbjlvh1.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