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- PDB-7n2t: O-acetylserine sulfhydrylase from Citrullus vulgaris in the inter... -

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Basic information

Entry
Database: PDB / ID: 7n2t
TitleO-acetylserine sulfhydrylase from Citrullus vulgaris in the internal aldimine state, with citrate bound
ComponentsCysteine synthase
KeywordsBIOSYNTHETIC PROTEIN / O-acetylserine sulfhydrylase / PLP / cysteine synthase
Function / homology
Function and homology information


beta-pyrazolylalanine synthase / L-mimosine synthase / pyrazolylalanine synthase / beta-pyrazolylalanine synthase activity / pyrazolylalanine synthase activity / L-mimosine synthase activity / cysteine synthase / cysteine synthase 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
CITRIC ACID / PHOSPHATE ION / Cysteine synthase
Similarity search - Component
Biological speciesCitrullus lanatus subsp. vulgaris (watermelon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSmith, J.L. / Buller, A.R. / Bingman, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM137417-01 United States
CitationJournal: Chembiochem / Year: 2022
Title: Investigation of beta-Substitution Activity of O-Acetylserine Sulfhydrolase from Citrullus vulgaris.
Authors: Smith, J.L. / Harrison, I.M. / Bingman, C.A. / Buller, A.R.
History
DepositionMay 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Apr 3, 2024Group: 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
A: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2044
Polymers35,6791
Non-polymers5253
Water3,765209
1
A: Cysteine synthase
hetero molecules

A: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4098
Polymers71,3582
Non-polymers1,0516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6040 Å2
ΔGint-41 kcal/mol
Surface area22130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.207, 63.591, 66.918
Angle α, β, γ (deg.)90.000, 91.450, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

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Components

#1: Protein Cysteine synthase / / CSase / Beta-PA/CSase / Beta-pyrazolylalanine synthase / L-mimosine synthase / O-acetylserine ...CSase / Beta-PA/CSase / Beta-pyrazolylalanine synthase / L-mimosine synthase / O-acetylserine (thiol)-lyase / OAS-TL / O-acetylserine sulfhydrylase


Mass: 35678.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrullus lanatus subsp. vulgaris (watermelon)
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q43317, cysteine synthase, beta-pyrazolylalanine synthase, pyrazolylalanine synthase, L-mimosine synthase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.2
Details: 29% PEG 300, 0.25 mM Citrate, 0.25 mM potassium phosphate pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 15, 2021
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. obs: 439646 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.7 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.11
Reflection shellResolution: 1.55→1.59 Å / Mean I/σ(I) obs: 1.49 / Num. unique obs: 30554 / CC1/2: 0.718

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 17ZY

17zy


Resolution: 1.55→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.6 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 3030 5.1 %RANDOM
Rwork0.1773 ---
obs0.178 56148 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.11 Å2 / Biso mean: 24.683 Å2 / Biso min: 15.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.21 Å2
2--0.16 Å20 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 34 209 2507
Biso mean--34.05 35.53 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132449
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172391
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.6383343
X-RAY DIFFRACTIONr_angle_other_deg1.2521.575530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.84422.78497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39715404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6451513
X-RAY DIFFRACTIONr_chiral_restr0.0540.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022813
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 242 -
Rwork0.356 4111 -
all-4353 -
obs--99.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4726-0.1205-1.4440.31820.05183.98880.0036-0.01120.0448-0.00010.0274-0.0192-0.1510.0678-0.0310.1213-0.0130.02340.075-0.00340.03050.6772.51524.893
21.07730.0482-0.1462.8211-0.45471.9747-0.0816-0.09290.01250.117-0.0342-0.08150.00330.07810.11580.09070.00480.02840.08540.010.0324-9.549-3.73728.483
32.5991-1.1177-0.79743.27820.8560.7693-0.007-0.0448-0.02260.0439-0.03710.224-0.0173-0.07960.04410.0857-0.00710.02290.08680.00520.0555-23.013-6.132.305
42.63550.2480.36266.19712.62242.5025-0.0124-0.0615-0.00670.0229-0.022-0.05650.0375-0.06480.03450.0865-0.01220.03540.06920.02010.0521-19.276-12.23635.284
58.95690.4949-1.46765.98842.74514.7217-0.08880.5891-0.7852-0.13790.0423-0.29760.29590.06430.04650.0757-0.00970.00970.0819-0.03240.0893-12.052-18.22734.942
62.4379-1.1302-1.12585.55631.32064.1936-0.05570.2406-0.1435-0.476-0.0640.23160.1024-0.15260.11970.1192-0.06140.01170.0651-0.02540.0742-24.882-21.81625.516
70.92980.3174-0.57151.0731-0.19621.04110.0440.10920.0515-0.0324-0.0010.1165-0.0908-0.1133-0.04290.11760.01150.01730.09270.01450.0182-14.3071.37718.442
89.57830.90076.46553.94773.597412.12380.44040.5251-1.2778-0.0979-0.18270.32431.2435-0.2856-0.25770.2983-0.0658-0.01670.0829-0.11980.2349-11.01-16.02810.727
90.8916-0.0176-0.07220.45770.00550.968600.1-0.1106-0.06370.03780.02050.0549-0.0001-0.03780.1304-0.00190.02050.0978-0.01210.0224-1.861-6.21613.294
1011.0989-18.9368-0.645578.7255-6.74031.3671-2.02820.6423-1.95671.10241.65431.5680.5359-0.48420.37390.5729-0.18240.2870.2674-0.36260.723-1.207-22.01527.562
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 40
2X-RAY DIFFRACTION2A41 - 54
3X-RAY DIFFRACTION3A55 - 85
4X-RAY DIFFRACTION4A86 - 103
5X-RAY DIFFRACTION5A104 - 118
6X-RAY DIFFRACTION6A119 - 139
7X-RAY DIFFRACTION7A140 - 211
8X-RAY DIFFRACTION8A212 - 228
9X-RAY DIFFRACTION9A229 - 303
10X-RAY DIFFRACTION10A304 - 314

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