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- PDB-6xgt: Crystal structure of cyanase from the thermophilic fungus Thermom... -

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Basic information

Entry
Database: PDB / ID: 6xgt
TitleCrystal structure of cyanase from the thermophilic fungus Thermomyces lanuginosus
ComponentsCyanate hydratase
KeywordsHYDROLASE / cyanase
Function / homologyFORMIC ACID / MALONATE ION
Function and homology information
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChoi, P.H. / Ranjan, B. / Tong, L.
Funding support South Africa, 1items
OrganizationGrant numberCountry
National Research Foundation in South AfricaUID 103232 South Africa
CitationJournal: Sci Rep / Year: 2021
Title: Crystal structure of a thermophilic fungal cyanase and its implications on the catalytic mechanism for bioremediation.
Authors: Ranjan, B. / Choi, P.H. / Pillai, S. / Permaul, K. / Tong, L. / Singh, S.
History
DepositionJun 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Cyanate hydratase
F: Cyanate hydratase
G: Cyanate hydratase
H: Cyanate hydratase
B: Cyanate hydratase
A: Cyanate hydratase
D: Cyanate hydratase
I: Cyanate hydratase
J: Cyanate hydratase
C: Cyanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,62917
Polymers201,13910
Non-polymers4907
Water14,358797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area66970 Å2
ΔGint-336 kcal/mol
Surface area51350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.368, 157.639, 163.871
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cyanate hydratase


Mass: 20113.863 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomyces lanuginosus (fungus) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2% (w/v) Tacsimate (pH 8.0), 0.1 M Tris (pH 8.5), and 16% (w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97856 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 99692 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.381 / Num. unique obs: 9819 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dw9

1dw9


Resolution: 2.2→45.36 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.541 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20182 4976 5 %RANDOM
Rwork0.15441 ---
obs0.15679 94642 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.645 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.2→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12520 0 33 798 13351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212876
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212360
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.97217415
X-RAY DIFFRACTIONr_angle_other_deg1.073328563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48751590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56224.259540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.048152220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4321560
X-RAY DIFFRACTIONr_chiral_restr0.1150.21910
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02114346
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022814
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_it2.3532.3256390
X-RAY DIFFRACTIONr_mcbond_other2.3532.3246391
X-RAY DIFFRACTIONr_mcangle_it3.7293.4687970
X-RAY DIFFRACTIONr_mcangle_other3.7293.4687971
X-RAY DIFFRACTIONr_scbond_it3.2962.6466486
X-RAY DIFFRACTIONr_scbond_other3.2872.6476476
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1613.8019446
X-RAY DIFFRACTIONr_long_range_B_refined8.01118.76115482
X-RAY DIFFRACTIONr_long_range_B_other8.01118.76115483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å
RfactorNum. reflection% reflection
Rfree0.255 338 -
Rwork0.197 6725 -
obs--96.79 %

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