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- PDB-8h41: Crystal structure of a decarboxylase from Trichosporon moniliifor... -

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Basic information

Entry
Database: PDB / ID: 8h41
TitleCrystal structure of a decarboxylase from Trichosporon moniliiforme in complex with o-nitrophenol
ComponentsSalicylate decarboxylase
KeywordsHYDROLASE / 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
O-NITROPHENOL / Salicylate decarboxylase
Similarity search - Component
Biological speciesCutaneotrichosporon moniliiforme (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsGao, J. / Zhao, Y.P. / Li, Q. / Liu, W.D. / Sheng, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Catalysts / Year: 2022
Title: A Combined Computational-Experimental Study on the Substrate Binding and Reaction Mechanism of Salicylic Acid Decarboxylase
Authors: Chen, F. / Zhao, Y. / Zhang, C. / Wang, W. / Gao, J. / Li, Q. / Qin, H. / Dai, Y. / Liu, W. / Liu, F. / Su, H. / Sheng, X.
History
DepositionOct 9, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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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)82,2996
Polymers81,9722
Non-polymers3274
Water14,826823
1
A: Salicylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1493
Polymers40,9861
Non-polymers1632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area14500 Å2
MethodPISA
2
B: Salicylate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1493
Polymers40,9861
Non-polymers1632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area14960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.916, 92.310, 128.660
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
11chain A
21(chain B and (resid -1 through 350 or resid 402))

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
11GLYGLYALAALAchain AAA-1 - 3507 - 358
21GLYGLYALAALA(chain B and (resid -1 through 350 or resid 402))BB-1 - 3507 - 358
22MGMGMGMG(chain B and (resid -1 through 350 or resid 402))BF402

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Components

#1: Protein Salicylate decarboxylase / Salicylic acid decarboxylase


Mass: 40986.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cutaneotrichosporon moniliiforme (fungus)
Gene: sdc / Plasmid: pQE80L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CT50, salicylate decarboxylase
#2: Chemical ChemComp-OPO / O-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 823 / 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: 2.1 Å3/Da / Density % sol: 41.37 % / Mosaicity: 1.247 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% w/v Poly(acrylic acid sodium salt) 5100, 0.02 M MgCl2, 0.1 M HEPES pH 7.5, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2021
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→30 Å / Num. obs: 64395 / % possible obs: 96.1 % / Redundancy: 5.9 % / Biso Wilson estimate: 17.05 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.041 / Rrim(I) all: 0.102 / Χ2: 1.873 / Net I/σ(I): 12.9 / Num. measured all: 382838
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.8460.59662040.7390.2610.6521.1493.9
1.84-1.926.10.44462600.8620.1920.4851.26294.3
1.92-26.10.33162640.9220.1430.3611.46994.9
2-2.1160.23763470.9590.1040.2591.67495.8
2.11-2.2460.18163840.9750.080.1991.88196.2
2.24-2.425.90.13664350.9850.060.1491.9996.7
2.42-2.665.80.10365270.9910.0460.1132.16397.7
2.66-3.045.80.07565390.9950.0340.0832.34597.2
3.04-3.835.70.05165740.9970.0230.0562.52497.1
3.83-3060.03868610.9980.0170.0422.26697.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JQW

6jqw


Resolution: 1.78→29.93 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 3212 5 %
Rwork0.1657 61027 -
obs0.1671 64239 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.92 Å2 / Biso mean: 19.0955 Å2 / Biso min: 7.28 Å2
Refinement stepCycle: final / Resolution: 1.78→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5720 0 22 823 6565
Biso mean--18.62 28.47 -
Num. residues----709
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2138X-RAY DIFFRACTION3.379TORSIONAL
12B2138X-RAY DIFFRACTION3.379TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.840.27893090.22935858616793
1.84-1.920.23723110.19145920623194
1.92-20.22233140.18295968628295
2-2.110.21233160.17286006632296
2.11-2.240.20593180.16346042636096
2.24-2.420.1983220.17076115643797
2.42-2.660.20393260.16346193651998
2.66-3.040.19983260.16226195652197
3.04-3.830.17033290.15276245657497
3.83-29.930.16463410.15566485682697

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