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- PDB-6mgs: Crystal structure of alpha-Amino-beta-Carboxymuconate-epsilon-Sem... -

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Basic information

Entry
Database: PDB / ID: 6mgs
TitleCrystal structure of alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase with Space Group of C2221
Components2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
KeywordsLYASE / Holo structure / decarboxylase
Function / homology
Function and homology information


organic substance metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding
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-amino-3-carboxymuconate 6-semialdehyde decarboxylase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.131 Å
AuthorsYang, Y. / Davis, I. / Matsui, T. / Rubalcava, I. / Liu, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM108988 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R21MH107985 United States
National Science Foundation (NSF, United States)CHE-1623856 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Quaternary structure of alpha-amino-beta-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) controls its activity.
Authors: Yang, Y. / Davis, I. / Matsui, T. / Rubalcava, I. / Liu, A.
History
DepositionSep 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 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)119,3296
Polymers119,1523
Non-polymers1773
Water19811
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)79,5534
Polymers79,4352
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
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)79,5534
Polymers79,4352
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.480, 154.170, 154.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 66 or resid 68...
21(chain B and (resid 4 through 66 or resid 68...
31(chain C and (resid 4 through 66 or resid 68...

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
11PROPROGLUGLU(chain A and (resid 4 through 66 or resid 68...AA4 - 6625 - 87
12ASPASPGLYGLY(chain A and (resid 4 through 66 or resid 68...AA68 - 14389 - 164
13GLNGLNALAALA(chain A and (resid 4 through 66 or resid 68...AA145 - 158166 - 179
14LEULEULEULEU(chain A and (resid 4 through 66 or resid 68...AA160 - 164181 - 185
15HISHISTRPTRP(chain A and (resid 4 through 66 or resid 68...AA166 - 244187 - 265
16HISHISASNASN(chain A and (resid 4 through 66 or resid 68...AA246 - 333267 - 354
21PROPROGLUGLU(chain B and (resid 4 through 66 or resid 68...BB4 - 6625 - 87
22ASPASPGLYGLY(chain B and (resid 4 through 66 or resid 68...BB68 - 14389 - 164
23GLNGLNTRPTRP(chain B and (resid 4 through 66 or resid 68...BB145 - 58166 - 79
24LYSLYSASNASN(chain B and (resid 4 through 66 or resid 68...BB3 - 33324 - 354
25HISHISTRPTRP(chain B and (resid 4 through 66 or resid 68...BB166 - 244187 - 265
26HISHISASNASN(chain B and (resid 4 through 66 or resid 68...BB246 - 333267 - 354
31PROPROGLUGLU(chain C and (resid 4 through 66 or resid 68...CC4 - 6625 - 87
32ASPASPGLYGLY(chain C and (resid 4 through 66 or resid 68...CC68 - 14389 - 164
33GLNGLNALAALA(chain C and (resid 4 through 66 or resid 68...CC145 - 158166 - 179
34LEULEULEULEU(chain C and (resid 4 through 66 or resid 68...CC160 - 164181 - 185
35HISHISTRPTRP(chain C and (resid 4 through 66 or resid 68...CC166 - 244187 - 265
36HISHISASNASN(chain C and (resid 4 through 66 or resid 68...CC246 - 333267 - 354

NCS oper:
IDCodeMatrixVector
1given(0.382798, -0.920917, 0.073329), (-0.921572, -0.386206, -0.039379), (0.064585, -0.052504, -0.99653)-57.310299, -86.588501, -20.643801
2given(0.354629, -0.93218, 0.07266), (0.931985, 0.358657, 0.052631), (-0.075121, 0.049054, 0.995967)-59.882999, 86.270798, 19.5651

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Components

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


Mass: 39717.332 Da / Num. of mol.: 3
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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6
Details: 8% (v/v) TacsimateTM pH 6.0 and 20% (w/v) polyethylene glycol 3,350
PH range: 6.0 -6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.12→50 Å / Num. obs: 21665 / % possible obs: 98.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 59.96 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.079 / Rrim(I) all: 0.163 / Χ2: 1.099 / Net I/σ(I): 4.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.12-3.173.80.95110590.7390.5641.1120.96197
3.17-3.233.70.72110000.8460.4310.8450.92894.6
3.23-3.294.10.73610970.8830.4150.8490.8898.7
3.29-3.364.50.64110590.8830.3430.7290.85299.5
3.36-3.434.50.60111050.8940.3240.6850.99299.4
3.43-3.514.60.51810750.9450.2760.5890.92599.5
3.51-3.64.60.45410550.9390.2440.5181.02299.6
3.6-3.74.50.38211040.9570.2050.4361.17699.5
3.7-3.814.60.30510750.9690.1620.3471.09499.4
3.81-3.934.60.30510840.9640.1630.3471.29499.3
3.93-4.074.50.23710740.9790.1280.271.03399.5
4.07-4.234.50.19410860.9770.1050.2211.08999.8
4.23-4.434.30.17411000.9820.0970.21.32699.1
4.43-4.664.10.15410660.980.0890.1791.44896.6
4.66-4.954.20.12710570.9880.0720.1471.30996.6
4.95-5.334.70.11410990.9910.0620.131.06199.6
5.33-5.874.60.11211020.990.060.1281.09599.3
5.87-6.724.50.111120.9910.0540.1141.05699.6
6.72-8.464.20.07211200.9940.0420.0841.13998.5
8.46-504.10.06311360.9930.0360.0731.30394.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX(1.11.1_2575)refinement
PDB_EXTRACT3.24data extraction
PHENIX1.10.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HBV

2hbv


Resolution: 3.131→34.491 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.42
RfactorNum. reflection% reflection
Rfree0.3005 1432 10.01 %
Rwork0.2293 --
obs0.2365 14306 65.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.72 Å2 / Biso mean: 57.8742 Å2 / Biso min: 9.89 Å2
Refinement stepCycle: final / Resolution: 3.131→34.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7752 0 3 11 7766
Biso mean--33.04 24.27 -
Num. residues----992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017967
X-RAY DIFFRACTIONf_angle_d1.22110796
X-RAY DIFFRACTIONf_chiral_restr0.0571148
X-RAY DIFFRACTIONf_plane_restr0.0071420
X-RAY DIFFRACTIONf_dihedral_angle_d15.8724747
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2537X-RAY DIFFRACTIONPOSITIONAL0.068
12B2537X-RAY DIFFRACTIONPOSITIONAL0.068
13C2537X-RAY DIFFRACTIONPOSITIONAL0.084
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 (%)
3.1308-3.24260.3405110.25681031145
3.2426-3.37230.428370.287932636317
3.3723-3.52570.3947780.318771078836
3.5257-3.71130.37031130.29041017113052
3.7113-3.94360.36831420.27271269141166
3.9436-4.24750.31831780.26241610178882
4.2475-4.67410.32812130.24061899211296
4.6741-5.34820.30522140.22251935214998
5.3482-6.730.29642200.22771983220399
6.73-34.49290.2112260.16442022224897

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