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

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Basic information

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


salicylate decarboxylase / organic substance metabolic process / carboxy-lyase activity / hydrolase activity
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
2-HYDROXYBENZOIC ACID / Salicylate decarboxylase
Similarity search - Component
Biological speciesCutaneotrichosporon moniliiforme (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.672 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 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,7216
Polymers80,3142
Non-polymers4074
Water15,241846
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-97 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.113, 93.863, 128.428
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -1 through 240 or resid 242 through 349 or resid 401))
21(chain B and (resid -1 through 240 or resid 242 through 349 or resid 401))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPHEPHE(chain A and (resid -1 through 240 or resid 242 through 349 or resid 401))AA-1 - 2401 - 242
12HISHISGLUGLU(chain A and (resid -1 through 240 or resid 242 through 349 or resid 401))AA242 - 349244 - 351
13SALSALSALSAL(chain A and (resid -1 through 240 or resid 242 through 349 or resid 401))AC401
21GLYGLYPHEPHE(chain B and (resid -1 through 240 or resid 242 through 349 or resid 401))BB-1 - 2401 - 242
22HISHISGLUGLU(chain B and (resid -1 through 240 or resid 242 through 349 or resid 401))BB242 - 349244 - 351
23SALSALSALSAL(chain B and (resid -1 through 240 or resid 242 through 349 or resid 401))BE401

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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CT50, salicylate decarboxylase
#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID / Salicylic acid


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 846 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG400, NaCl / PH range: 8.5

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→25 Å / Num. obs: 81338 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.039 / Rrim(I) all: 0.11 / Χ2: 0.721 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.67-1.7360.60580130.8480.2620.6620.51699.9
1.73-1.87.30.51880330.9140.2030.5570.554100
1.8-1.887.70.37480500.9590.1430.40.608100
1.88-1.987.80.26580500.9780.10.2840.707100
1.98-2.17.90.18580680.9870.0690.1980.841100
2.1-2.2780.14580890.9920.0540.1550.97100
2.27-2.4980.11181000.9940.0410.1190.802100
2.49-2.858.10.0981610.9960.0330.0960.752100
2.85-3.598.20.07382460.9970.0270.0770.834100
3.59-257.90.05785280.9980.0210.0610.54399.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dvt

2dvt


Resolution: 1.672→24.775 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.37
RfactorNum. reflection% reflection
Rfree0.1735 2000 2.46 %
Rwork0.1545 --
obs0.155 81249 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.75 Å2 / Biso mean: 19.3099 Å2 / Biso min: 9.64 Å2
Refinement stepCycle: final / Resolution: 1.672→24.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5664 0 22 846 6532
Biso mean--28.25 31.65 -
Num. residues----703
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2119X-RAY DIFFRACTION6.545TORSIONAL
12B2119X-RAY DIFFRACTION6.545TORSIONAL
Refinement TLS params.Method: refined / Origin x: 27.6 Å / Origin y: 1.652 Å / Origin z: 3.261 Å
111213212223313233
T0.2697 Å20.0043 Å2-0.0074 Å2-0.067 Å20.01 Å2--0.0343 Å2
L0.1906 °2-0.0174 °2-0.0373 °2-0.6079 °20.2319 °2--0.6192 °2
S0.0048 Å °-0.0083 Å °0.0074 Å °0.0293 Å °-0.0164 Å °0.0104 Å °-0.0287 Å °-0.0071 Å °0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 350
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION1B-1 - 349
4X-RAY DIFFRACTION1B401
5X-RAY DIFFRACTION1A402
6X-RAY DIFFRACTION1B402
7X-RAY DIFFRACTION1A501 - 951
8X-RAY DIFFRACTION1B501 - 895

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