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- PDB-5d2h: 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - compl... -

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Basic information

Entry
Database: PDB / ID: 5d2h
Title4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - complexed with magnesium and alpha-ketoglutarate
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 / 2-OXOGLUTARIC ACID / 4-oxalocrotonate decarboxylase NahK
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.936 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)31,66615
Polymers30,7461
Non-polymers92014
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.741, 44.904, 125.318
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 , 7 types, 284 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 38.54 % / 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: 1.936→42.272 Å / Num. obs: 18138 / % possible obs: 94.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 21.52 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 9.868
Reflection shellResolution: 1.936→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 1.388 / % possible all: 70.7

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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: 1.936→42.272 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 918 5.07 %Random selection
Rwork0.1632 ---
obs0.1667 18095 94.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.62 Å2
Refinement stepCycle: LAST / Resolution: 1.936→42.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 57 270 2315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072084
X-RAY DIFFRACTIONf_angle_d1.0972811
X-RAY DIFFRACTIONf_dihedral_angle_d13.111759
X-RAY DIFFRACTIONf_chiral_restr0.068322
X-RAY DIFFRACTIONf_plane_restr0.004366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.936-2.03810.31571140.25931865X-RAY DIFFRACTION73
2.0381-2.16580.26481240.21282345X-RAY DIFFRACTION92
2.1658-2.3330.24511300.17192543X-RAY DIFFRACTION99
2.333-2.56770.28391220.17572577X-RAY DIFFRACTION100
2.5677-2.93920.22821470.16872561X-RAY DIFFRACTION100
2.9392-3.70270.23441420.14282618X-RAY DIFFRACTION100
3.7027-42.28220.18211390.1412668X-RAY DIFFRACTION97

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