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- PDB-5b55: Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) D... -

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Basic information

Entry
Database: PDB / ID: 5b55
TitleCrystal structure of hydrogen sulfide-producing enzyme (Fn1055) D232N mutant in complexed with alpha-aminoacrylate intermediate: lysine-dimethylated form
ComponentsCysteine synthase
KeywordsTRANSFERASE / Pyridoxal 5'-phosphate dependent enzyme / alpha-Aminoacrylate
Function / homology
Function and homology information


L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / : / cytoplasm
Similarity search - Function
: / 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
Chem-0JO / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Cysteine synthase
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum strain ATCC 25586 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsKezuka, Y. / Yoshida, Y. / Nonaka, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science21791810 Japan
Japan Society for the Promotion of Science23792130 Japan
CitationJournal: Biochem. J. / Year: 2018
Title: Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen,Fusobacterium nucleatum.
Authors: Kezuka, Y. / Ishida, T. / Yoshida, Y. / Nonaka, T.
History
DepositionApr 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
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 / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,4678
Polymers77,1282
Non-polymers1,3396
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-17 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.046, 57.127, 94.293
Angle α, β, γ (deg.)90.00, 100.89, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 3 - 334 / Label seq-ID: 7 - 338

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cysteine synthase


Mass: 38564.113 Da / Num. of mol.: 2 / Mutation: D232N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum strain ATCC 25586 (bacteria)
Strain: ATCC 25586 / Gene: FN1055 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8REP3, cysteine synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13N2O7P
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24% (w/v) PEG3350, 0.1M Hepes pH 7.5, 0.2M Magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→60.43 Å / Num. obs: 52807 / % possible obs: 95.6 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.8
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 7.3 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B53

5b53


Resolution: 2.14→36.66 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.445 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 2648 5 %RANDOM
Rwork0.20106 ---
obs0.20288 50143 95.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.482 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å2-1.44 Å2
2---0.79 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.14→36.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5241 0 86 319 5646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.025453
X-RAY DIFFRACTIONr_bond_other_d0.0070.025302
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9847341
X-RAY DIFFRACTIONr_angle_other_deg1.362.98312302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03225.305213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.988151077
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1241520
X-RAY DIFFRACTIONr_chiral_restr0.2780.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025953
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021101
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_it2.1082.1842684
X-RAY DIFFRACTIONr_mcbond_other2.1092.1852680
X-RAY DIFFRACTIONr_mcangle_it3.0683.2643351
X-RAY DIFFRACTIONr_mcangle_other3.0683.2663350
X-RAY DIFFRACTIONr_scbond_it2.9662.6232769
X-RAY DIFFRACTIONr_scbond_other2.9632.6232769
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6753.753985
X-RAY DIFFRACTIONr_long_range_B_refined6.27317.6976432
X-RAY DIFFRACTIONr_long_range_B_other6.19817.5486324
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 42386 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 182 -
Rwork0.203 3684 -
obs--95.03 %

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