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- PDB-6jqw: Crystal structure of a hydrogenase from Trichosporon moniliiforme -

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Basic information

Entry
Database: PDB / ID: 6jqw
TitleCrystal structure of a hydrogenase from Trichosporon moniliiforme
ComponentsSalicylate decarboxylase
KeywordsHYDROLASE / Structure function / Salicylate / decarboxylase
Function / homology
Function and homology information


salicylate decarboxylase / secondary metabolic process / : / : / carboxy-lyase activity / hydrolase activity / cytosol
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Salicylate decarboxylase
Similarity search - Component
Biological speciesCutaneotrichosporon moniliiforme (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.437 Å
AuthorsQin, H.M. / Chen, X.T.
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Structural Basis of Salicylic Acid Decarboxylase Reveals a Unique Substrate Recognition Mode and Access Channel.
Authors: Gao, X. / Wu, M. / Zhang, W. / Li, C. / Guo, R.T. / Dai, Y. / Liu, W. / Mao, S. / Lu, F. / Qin, H.M.
History
DepositionApr 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: Salicylate decarboxylase
B: Salicylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4454
Polymers80,3142
Non-polymers1312
Water14,934829
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-100 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.691, 93.763, 128.811
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 Salicylate decarboxylase / Salicylic acid decarboxylase


Mass: 40157.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cutaneotrichosporon moniliiforme (fungus)
Gene: sdc / Plasmid: pQE-80L / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CT50, salicylate decarboxylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 829 / 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: 2.17 Å3/Da / Density % sol: 43.29 % / Mosaicity: 0.603 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG400, NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 20, 2018
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.437→25 Å / Num. obs: 127185 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.032 / Rrim(I) all: 0.089 / Χ2: 0.888 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.44-1.496.40.573125630.8830.2350.6210.44299.8
1.49-1.557.20.459125780.9230.180.4930.464100
1.55-1.627.30.336125640.960.1310.3620.495100
1.62-1.717.40.259126330.9750.10.2780.543100
1.71-1.817.50.194126340.9840.0750.2080.604100
1.81-1.957.60.136126400.9920.0520.1450.703100
1.95-2.157.80.097127130.9950.0370.1030.898100
2.15-2.468.10.078127400.9960.0290.0841.133100
2.46-3.18.20.061128410.9980.0230.0651.391100
3.1-257.90.05132790.9980.0190.0531.87799.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dvt

2dvt


Resolution: 1.437→24.842 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.72
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 1999 1.57 %RANDOM
Rwork0.1522 ---
obs0.1526 127071 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.437→24.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5670 0 2 829 6501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085838
X-RAY DIFFRACTIONf_angle_d1.0527904
X-RAY DIFFRACTIONf_dihedral_angle_d12.1192132
X-RAY DIFFRACTIONf_chiral_restr0.087792
X-RAY DIFFRACTIONf_plane_restr0.0081044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4371-1.47310.21631340.20048412X-RAY DIFFRACTION95
1.4731-1.51290.19551420.17848887X-RAY DIFFRACTION100
1.5129-1.55740.20761430.16528869X-RAY DIFFRACTION100
1.5574-1.60770.20191410.15538857X-RAY DIFFRACTION100
1.6077-1.66510.17821420.14758891X-RAY DIFFRACTION100
1.6651-1.73180.17931430.14698901X-RAY DIFFRACTION100
1.7318-1.81060.18081420.14658931X-RAY DIFFRACTION100
1.8106-1.9060.17531420.1478931X-RAY DIFFRACTION100
1.906-2.02540.16731420.14488914X-RAY DIFFRACTION100
2.0254-2.18170.17731440.14338964X-RAY DIFFRACTION100
2.1817-2.4010.17761440.15239005X-RAY DIFFRACTION100
2.401-2.74810.19641450.16259036X-RAY DIFFRACTION100
2.7481-3.46080.17441450.15659091X-RAY DIFFRACTION100
3.4608-24.84530.15671500.14269383X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 27.5399 Å / Origin y: 1.5901 Å / Origin z: 3.1792 Å
111213212223313233
T0.2037 Å20.0012 Å2-0.0062 Å2-0.0448 Å20.0205 Å2--0.0194 Å2
L0.2839 °2-0.0342 °2-0.053 °2-0.7275 °20.2492 °2--0.4253 °2
S0.0012 Å °-0.0005 Å °0.0011 Å °0.0337 Å °-0.0199 Å °0.0109 Å °-0.0122 Å °-0.0056 Å °0.0116 Å °
Refinement TLS groupSelection details: all

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