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- PDB-8yt2: Crystal structure of ACMSD mutant W194A -

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Basic information

Entry
Database: PDB / ID: 8yt2
TitleCrystal structure of ACMSD mutant W194A
Components2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
KeywordsLYASE / kynurenine / decarboxylase / NAD homeostasis / tryptophan metabolism / metalloenzyme
Function / homology
Function and homology information


aminocarboxymuconate-semialdehyde decarboxylase / secondary metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsYang, Y. / Liu, A.
Funding support United States, China, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA270879 United States
Welch FoundationAX-2110-20220331 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG078775 United States
National Science Foundation (NSF, China)32101016 China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: alpha-Amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase catalyzes enol/keto tautomerization of oxaloacetate.
Authors: Yang, Y. / Davis, I. / Altman, R.A. / Liu, A.
History
DepositionMar 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
B: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
C: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4026
Polymers111,2053
Non-polymers1963
Water11,872659
1
A: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
hetero molecules

A: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2684
Polymers74,1372
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5100 Å2
ΔGint-113 kcal/mol
Surface area23720 Å2
MethodPISA
2
B: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
C: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2684
Polymers74,1372
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-109 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.002, 151.647, 154.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

21A-611-

HOH

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Components

#1: Protein 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase / Alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase / ACMSD


Mass: 37068.465 Da / Num. of mol.: 3 / Mutation: W194A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: nbaD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q83V25
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 295 K / Method: evaporation
Details: 2% (v/v) malonate pH 7.0, 0.1M sodium citrate tribasic pH 5.6, 12% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 79968 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 1 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.02-2.055.90.95539480.7130.9120.4231.0470.72599.6
2.05-2.096.20.83139890.7190.9140.3590.9070.88399.7
2.09-2.136.90.68439160.8580.9610.280.740.7799.9
2.13-2.187.30.61539520.8830.9680.2450.6630.79199.9
2.18-2.227.30.53439800.9160.9780.2110.5750.806100
2.22-2.277.30.52239720.9150.9780.2080.5621.006100
2.27-2.337.40.40539670.9550.9880.160.4350.867100
2.33-2.397.40.36939610.9560.9890.1460.3970.893100
2.39-2.477.40.32739500.9670.9920.1290.3520.92100
2.47-2.547.40.27840210.9750.9940.1090.2990.982100
2.54-2.647.40.23839820.980.9950.0940.2561.012100
2.64-2.747.40.2139830.9830.9960.0830.2261.114100
2.74-2.877.40.17339850.9880.9970.0680.1861.093100
2.87-3.027.40.15539790.9890.9970.0610.1661.183100
3.02-3.217.30.12340300.9930.9980.0490.1321.183100
3.21-3.457.20.09940180.9950.9990.040.1071.288100
3.45-3.87.10.08240260.9960.9990.0330.0891.255100
3.8-4.3570.0740470.9960.9990.0290.0761.172100
4.35-5.486.90.06340790.9970.9990.0260.0681.068100
5.48-506.50.06641830.9940.9990.0290.0721.08398.7

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→43.1 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1998 2.5 %
Rwork0.1943 --
obs0.1952 79920 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7666 0 3 659 8328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087890
X-RAY DIFFRACTIONf_angle_d0.85810692
X-RAY DIFFRACTIONf_dihedral_angle_d8.1381043
X-RAY DIFFRACTIONf_chiral_restr0.0531145
X-RAY DIFFRACTIONf_plane_restr0.0061407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.070.32181360.28335358X-RAY DIFFRACTION97
2.07-2.120.31371410.25815486X-RAY DIFFRACTION100
2.12-2.190.28381420.23825566X-RAY DIFFRACTION100
2.19-2.260.27391420.23475530X-RAY DIFFRACTION100
2.26-2.340.25871420.22435512X-RAY DIFFRACTION100
2.34-2.430.28091420.21415559X-RAY DIFFRACTION100
2.43-2.540.24021430.21265560X-RAY DIFFRACTION100
2.54-2.680.23421420.20895532X-RAY DIFFRACTION100
2.68-2.840.25921430.21215579X-RAY DIFFRACTION100
2.84-3.060.28161430.2195598X-RAY DIFFRACTION100
3.06-3.370.23991430.19915575X-RAY DIFFRACTION100
3.37-3.860.20041450.18045623X-RAY DIFFRACTION100
3.86-4.860.19431450.15285658X-RAY DIFFRACTION100
4.86-43.10.18161490.16195786X-RAY DIFFRACTION99

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