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- PDB-5d2f: 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - apo form -

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Basic information

Entry
Database: PDB / ID: 5d2f
Title4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - apo form
Components4-oxalocrotonate decarboxylase NahK
KeywordsLYASE / naphthalene degradation
Function / homology
Function and homology information


catalytic activity / metal ion binding
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 family / 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: 1.738 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 / 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

Downloads & links

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Assembly

Deposited unit
A: 4-oxalocrotonate decarboxylase NahK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,62116
Polymers30,7461
Non-polymers87515
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.763, 44.939, 125.141
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2 Å3/Da / Density % sol: 38.6 % / 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: 1.7378→31.3577 Å / Num. obs: 25510 / % possible obs: 97.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 15.42 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.237
Reflection shellResolution: 1.7378→1.78 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 2.82 / % possible all: 94.5

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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: 1.738→31.353 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 1302 5.14 %Random selection
Rwork0.1681 ---
obs0.1703 25312 96.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.49 Å2
Refinement stepCycle: LAST / Resolution: 1.738→31.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 54 388 2430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072091
X-RAY DIFFRACTIONf_angle_d1.1742818
X-RAY DIFFRACTIONf_dihedral_angle_d12.573766
X-RAY DIFFRACTIONf_chiral_restr0.077324
X-RAY DIFFRACTIONf_plane_restr0.004366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7378-1.80730.29171360.22612534X-RAY DIFFRACTION94
1.8073-1.88960.27151380.22332599X-RAY DIFFRACTION95
1.8896-1.98920.25641480.20362582X-RAY DIFFRACTION96
1.9892-2.11380.18081540.15052615X-RAY DIFFRACTION97
2.1138-2.27690.21521320.20152580X-RAY DIFFRACTION94
2.2769-2.5060.24721320.16742710X-RAY DIFFRACTION98
2.506-2.86840.22751550.1682704X-RAY DIFFRACTION99
2.8684-3.6130.18571430.14272765X-RAY DIFFRACTION99
3.613-31.35770.17821640.15042921X-RAY DIFFRACTION99
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)
10.73960.0232-0.21711.2025-0.48351.01560.0035-0.02030.0981-0.07680.00880.0067-0.13560.0724-0.00590.0999-0.0149-0.01010.0797-0.01390.090223.097521.615219.9174
20.77450.40080.54080.61650.06080.8526-0.0272-0.04850.0251-0.0326-0.0085-0.0005-0.04290.0110.03850.0883-0.00170.00730.0802-0.00930.078818.688212.286912.3785
30.42040.16850.18510.2229-0.07190.99720.0306-0.0307-0.005-0.0062-0.00370.01520.0298-0.0742-0.01580.08190.0065-0.00340.0813-0.00070.095613.78475.592114.6666
40.5851-0.00090.11330.5316-0.41420.84670.0374-0.0448-0.1548-0.05840.04150.01530.2334-0.3674-0.00490.145-0.0546-0.0220.18670.02220.13611.2353-3.863712.7449
50.1173-0.05610.11070.1635-0.07930.72520.0182-0.0283-0.0488-0.0310.018-0.00290.154-0.11-0.0320.1061-0.01-0.01680.10460.00550.104810.60131.435413.3521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 171 )
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 207 )
5X-RAY DIFFRACTION5chain 'A' and (resid 208 through 264 )

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