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- PDB-7djq: Crystal Structure of O-acetyl L-serine sulfhydrylase from Haemoph... -

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Basic information

Entry
Database: PDB / ID: 7djq
TitleCrystal Structure of O-acetyl L-serine sulfhydrylase from Haemophilus influenzae in complex with C-Terminal peptide of ribosomal S4 Domain protein from Lactobacillus salivarius.
Components
  • C-Terminal peptide of ribosomal S4 Domain protein
  • Cysteine synthase
KeywordsTRANSFERASE / Complex / Enzyme / inhibitor
Function / homology
Function and homology information


L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / RNA binding / cytoplasm
Similarity search - Function
RNA-binding protein, HP1423 type / 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / S4 RNA-binding domain profile. ...RNA-binding protein, HP1423 type / 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily
Similarity search - Domain/homology
RNA-binding S4 domain-containing protein / Cysteine synthase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
Lactobacillus salivarius UCC118 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSaini, N. / Rahisuddin, R. / Kumaran, S.
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Moonlighting Biochemistry of Cysteine Synthase: A Species-specific Global Regulator.
Authors: Singh, R.P. / Saini, N. / Sharma, G. / Rahisuddin, R. / Patel, M. / Kaushik, A. / Kumaran, S.
History
DepositionNov 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: C-Terminal peptide of ribosomal S4 Domain protein
B: Cysteine synthase
A: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7466
Polymers75,6773
Non-polymers693
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-56 kcal/mol
Surface area22260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.080, 98.940, 70.290
Angle α, β, γ (deg.)90.000, 95.770, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide C-Terminal peptide of ribosomal S4 Domain protein


Mass: 1188.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lactobacillus salivarius UCC118 (bacteria) / References: UniProt: A0A1V9TQZ2
#2: Protein Cysteine synthase / O-acetyl L-serine sulfhydrylase / CSase / O-acetylserine (thiol)-lyase / OAS-TL / O-acetylserine sulfhydrylase


Mass: 37244.453 Da / Num. of mol.: 2 / Mutation: D67E/A68P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Gene: cysK, HI_1103
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P45040, cysteine synthase
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 100mM HEPES buffer pH 7.4, 1.4M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 19, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40.86 Å / Num. obs: 28307 / % possible obs: 97.66 % / Redundancy: 15.2 % / Biso Wilson estimate: 19.86 Å2 / CC1/2: 0.855 / CC star: 0.96 / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.1
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 9 % / Rmerge(I) obs: 0.15 / Num. unique obs: 2705 / CC1/2: 0.826 / CC star: 0.951 / % possible all: 94.98

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HO1

4ho1


Resolution: 2.3→40.86 Å / SU ML: 0.2184 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1909 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2286 1351 4.85 %
Rwork0.1893 26526 -
obs0.1912 27877 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4455 0 3 125 4583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01474522
X-RAY DIFFRACTIONf_angle_d1.51636140
X-RAY DIFFRACTIONf_chiral_restr0.0811734
X-RAY DIFFRACTIONf_plane_restr0.0093787
X-RAY DIFFRACTIONf_dihedral_angle_d5.03622737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.26451270.19262578X-RAY DIFFRACTION94.98
2.38-2.480.24391210.19262594X-RAY DIFFRACTION94.86
2.48-2.590.25271280.19622570X-RAY DIFFRACTION95.57
2.59-2.730.25861500.2072577X-RAY DIFFRACTION96.33
2.73-2.90.24751280.19792639X-RAY DIFFRACTION97.4
2.9-3.120.24511590.20582670X-RAY DIFFRACTION99.02
3.12-3.440.21751330.20842695X-RAY DIFFRACTION99.54
3.44-3.930.21231240.16992732X-RAY DIFFRACTION99.55
3.93-4.950.19621410.1622712X-RAY DIFFRACTION99.83
4.95-100.22381400.19812759X-RAY DIFFRACTION99.72

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