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- PDB-7k12: ACMSD in complex with diflunisal -

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Basic information

Entry
Database: PDB / ID: 7k12
TitleACMSD in complex with diflunisal
Components2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
KeywordsLYASE / FDA-approved drugs / NAD+ / neuropsychiatric disorders / decarboxylase
Function / homology
Function and homology information


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
5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID / CITRIC ACID / 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsYang, Y. / Liu, A.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1623856 United States
National Science Foundation (NSF, United States)CHE-1808637 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108988 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133721 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)MH107985 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Diflunisal Derivatives as Modulators of ACMS Decarboxylase Targeting the Tryptophan-Kynurenine Pathway.
Authors: Yang, Y. / Borel, T. / de Azambuja, F. / Johnson, D. / Sorrentino, J.P. / Udokwu, C. / Davis, I. / Liu, A. / Altman, R.A.
History
DepositionSep 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 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
A: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
B: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1356
Polymers79,4352
Non-polymers7004
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-72 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.588, 93.588, 445.743
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-675-

HOH

21A-693-

HOH

31B-531-

HOH

41B-647-

HOH

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Components

#1: Protein 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase


Mass: 39717.332 Da / Num. of mol.: 2
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, Lyases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-1FL / 5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID / Diflunisal


Mass: 250.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H8F2O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory*YM
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 3.55 Å3/Da / Density % sol: 65.32 %
Crystal growTemperature: 297 K / Method: evaporation / pH: 6.4 / Details: 0.4 M ammonium citrate, pH 6.4, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 20, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 62641 / % possible obs: 99.7 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.045 / Rrim(I) all: 0.14 / Χ2: 1.175 / Net I/σ(I): 4 / Num. measured all: 532757
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.17-2.218.40.95730370.8150.3311.0171.18100
2.21-2.258.50.86630550.7970.30.9211.36499.7
2.25-2.298.40.72630710.8940.2530.7731.40499.5
2.29-2.348.20.62230530.90.2190.6621.18999.4
2.34-2.397.40.52730530.9090.1950.5651.19999.8
2.39-2.448.30.45830510.9620.1590.4871.214100
2.44-2.519.10.48630880.9390.1620.5141.207100
2.51-2.579.10.3730840.970.1220.3911.216100
2.57-2.6590.33630900.9690.1110.3551.23199.9
2.65-2.738.90.33230930.9680.1110.3521.429100
2.73-2.838.90.25831160.9840.0850.2731.20299.9
2.83-2.958.80.21531190.9840.0710.2271.18599.9
2.95-3.088.80.19130930.9890.0630.2021.14399.9
3.08-3.248.40.14731370.9950.0490.1551.12899.6
3.24-3.447.60.12531220.9910.0440.1331.21399.1
3.44-3.718.40.131550.9960.0330.1061.21899.9
3.71-4.088.90.09131990.9970.030.0961.17999.9
4.08-4.678.80.0832230.9950.0270.0851.0899.7
4.67-5.898.30.06732580.9970.0230.0710.88299.1
5.89-507.80.0535440.9980.0180.0540.66899

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
PHENIX1.17.1-3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HBV

2hbv


Resolution: 2.17→45.8 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1997 3.2 %
Rwork0.2005 60337 -
obs0.2015 62334 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.74 Å2 / Biso mean: 47.0601 Å2 / Biso min: 25.98 Å2
Refinement stepCycle: final / Resolution: 2.17→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5174 0 45 422 5641
Biso mean--56.89 49.52 -
Num. residues----662
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.17-2.220.37481390.327941944333100
2.22-2.280.31991400.32624202434299
2.28-2.350.32611390.29044190432999
2.35-2.430.30921380.26444210434899
2.43-2.510.30161400.255442404380100
2.51-2.610.30771420.240742714413100
2.61-2.730.26241400.235442464386100
2.73-2.880.26461430.22342804423100
2.88-3.060.27171420.229643184460100
3.06-3.290.22821420.21094284442699
3.29-3.620.22561440.19634346449099
3.62-4.150.21661450.166643764521100
4.15-5.220.17081480.149944684616100
5.23-45.80.18271550.16724712486798

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