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- PDB-9jxu: Crystal structure of cysteine synthase A from Limosilactobacillus... -

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Basic information

Entry
Database: PDB / ID: 9jxu
TitleCrystal structure of cysteine synthase A from Limosilactobacillus reuteri LR1 in its apo form
ComponentsCysteine synthase
KeywordsLYASE / cysteine synthase / LreCysK / CysK / apo form
Function / homology
Function and homology information


cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine
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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cysteine synthase
Similarity search - Component
Biological speciesLimosilactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMatyuta, I.O. / Les, E.K. / Minyaev, M.E. / Pometun, A.A. / Tishkov, V.I. / Popov, V.O. / Boyko, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure-functional examination of novel cysteine synthase A (CysK) from Limosilactobacillus reuteri LR1
Authors: Shaposhnikov, E.K. / Les, E.K. / Chikurova, N.Y. / Matyuta, I.O. / Boyko, K.M. / Minyaev, M.E. / Popov, V.O. / Gorbovskaia, A.V. / Shirokova, A.A. / Loginova, A.A. / Savin, S.S. / Kleymenov, ...Authors: Shaposhnikov, E.K. / Les, E.K. / Chikurova, N.Y. / Matyuta, I.O. / Boyko, K.M. / Minyaev, M.E. / Popov, V.O. / Gorbovskaia, A.V. / Shirokova, A.A. / Loginova, A.A. / Savin, S.S. / Kleymenov, S.Y. / Chernobrovkina, A.V. / Pometun, E.V. / Tishkov, V.I. / Pometun, A.A.
History
DepositionOct 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Structure summary / Category: audit_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine synthase
B: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,34514
Polymers66,3322
Non-polymers1,01312
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-73 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.642, 101.292, 63.530
Angle α, β, γ (deg.)90.00, 107.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cysteine synthase


Mass: 33166.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus reuteri (bacteria)
Gene: cysK, B1A73_08060, B5F04_07160, B5G22_06315, GTO86_10515
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1S9AE02, cysteine synthase

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Non-polymers , 5 types, 98 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Lithium sulfate monohydrate, 0.1 M Citric acid pH 3.5, 18% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.2→20.4 Å / Num. obs: 32499 / % possible obs: 98.9 % / Redundancy: 4.8 % / CC1/2: 0.973 / Rmerge(I) obs: 0.273 / Rpim(I) all: 0.139 / Rrim(I) all: 0.308 / Χ2: 0.97 / Net I/σ(I): 5.4 / Num. measured all: 155579
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 98.1 % / Redundancy: 5 % / Rmerge(I) obs: 1.331 / Num. measured all: 14032 / Num. unique obs: 2783 / CC1/2: 0.412 / Rpim(I) all: 0.657 / Rrim(I) all: 1.489 / Χ2: 1.01 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XOQ

5xoq


Resolution: 2.2→20.4 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.887 / SU B: 8.527 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27136 1583 4.9 %RANDOM
Rwork0.21156 ---
obs0.21452 30892 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.791 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20.26 Å2
2---0.64 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 2.2→20.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3953 0 61 86 4100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124086
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9371.8035538
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1125557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.95158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.81210628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2460.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023000
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3153.2442222
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.575.8272769
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.6283.5021864
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.36637.635873
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 106 -
Rwork0.312 2244 -
obs--98 %

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