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- PDB-5d2g: 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - compl... -

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Basic information

Entry
Database: PDB / ID: 5d2g
Title4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - complexed with magnesium
Components4-oxalocrotonate decarboxylase NahK
KeywordsLYASE / naphthalene degradation
Function / homology
Function and homology information


2-oxopent-4-enoate hydratase activity / catabolic process / metal ion binding / cytoplasm
Similarity search - Function
4-oxalocrotonate decarboxylase / : / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase C-terminal / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 4-oxalocrotonate decarboxylase NahK
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å
AuthorsGuimaraes, S.L. / Nagem, R.A.P.
Funding support Brazil, 4items
OrganizationGrant numberCountry
CAPES Brazil
FAPEMIGRDP-00174-10; EDT-0185-0.00-0; Rede-170/08 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)482173/2010-6 Brazil
VALE S.A.RDP-00174-10 Brazil
CitationJournal: Biochemistry / Year: 2016
Title: Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous beta-Keto Acid.
Authors: Guimaraes, S.L. / Coitinho, J.B. / Costa, D.M. / Araujo, S.S. / Whitman, C.P. / Nagem, R.A.
History
DepositionAug 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-oxalocrotonate decarboxylase NahK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,49314
Polymers30,7461
Non-polymers74713
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.766, 45.035, 124.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 4-oxalocrotonate decarboxylase NahK


Mass: 30746.088 Da / Num. of mol.: 1 / Mutation: L155P
Source method: isolated from a genetically manipulated source
Details: from plasmid NAH7 / Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: nahK / Plasmid: pET28a-TEV
Details (production host): The thrombin site in the original pET28a vector was replaced by the TEV site for tag cleavage
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q1XGK3, 2-oxo-3-hexenedioate decarboxylase

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Non-polymers , 6 types, 315 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37 % / Description: parallelepiped-shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: lithium sulfate monohydrate / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.437 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.437 Å / Relative weight: 1
ReflectionResolution: 1.897→40.452 Å / Num. obs: 18966 / % possible obs: 95.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 18.79 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.2
Reflection shellResolution: 1.897→1.96 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 1.828 / % possible all: 72.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EB4

2eb4


Resolution: 1.897→40.452 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.204 951 5.03 %Random selection
Rwork0.1535 ---
obs0.1561 18912 95.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.98 Å2
Refinement stepCycle: LAST / Resolution: 1.897→40.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 44 302 2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082060
X-RAY DIFFRACTIONf_angle_d1.2112783
X-RAY DIFFRACTIONf_dihedral_angle_d12.038746
X-RAY DIFFRACTIONf_chiral_restr0.077321
X-RAY DIFFRACTIONf_plane_restr0.005361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8968-1.99680.29141130.25712048X-RAY DIFFRACTION78
1.9968-2.12190.26061340.19482559X-RAY DIFFRACTION97
2.1219-2.28570.22381410.15752630X-RAY DIFFRACTION100
2.2857-2.51570.19351210.15232662X-RAY DIFFRACTION99
2.5157-2.87970.22121550.15372593X-RAY DIFFRACTION98
2.8797-3.62770.20241390.13962662X-RAY DIFFRACTION98
3.6277-40.46120.16011480.13422807X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.38420.9916-1.52267.5892-5.65545.49790.10180.02180.06650.1419-0.1194-0.1889-0.22870.2681-0.00160.0936-0.0053-0.00120.14-0.03250.066725.341820.803717.4591
22.0376-0.55230.66331.4487-0.28653.25840.0010.05560.0847-0.04390.0161-0.0075-0.1198-0.0015-0.01520.081-0.04030.01190.0584-0.00250.066421.583918.198617.1329
33.60230.67171.74421.2139-0.21563.51930.1041-0.13880.4365-0.0251-0.06350.1297-0.1063-0.3267-0.00170.1113-0.00810.03370.1117-0.03660.08899.140311.765411.2392
40.91810.27920.42450.8181-0.27752.310.0670.0229-0.00460.03-0.02990.07880.1402-0.0971-0.02990.05220.00840.0110.0830.00630.089713.19754.933114.8787
52.1895-0.27450.0691.95420.3195.0877-0.01340.3245-0.177-0.33090.0204-0.07310.4329-0.43180.00670.21-0.0883-0.0240.1549-0.00650.14931.992-6.915812.0622
60.1620.0438-0.39760.4599-0.76163.02520.0398-0.0277-0.02640.01730.01830.0330.0249-0.0658-0.06660.08630.0066-0.01570.10930.00270.08898.04184.885410.7796
75.13421.59993.99993.1452.39176.30030.1961-0.3489-0.4173-0.06490.07440.07570.58-0.4321-0.2640.1976-0.0273-0.02120.11820.04230.11746.0527-7.631122.2748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 81 )
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 170 )
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 193 )
6X-RAY DIFFRACTION6chain 'A' and (resid 194 through 247 )
7X-RAY DIFFRACTION7chain 'A' and (resid 248 through 264 )

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