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- PDB-5d2k: 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - compl... -

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Basic information

Entry
Database: PDB / ID: 5d2k
Title4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - complexed with magnesium and 2-oxoadipate
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 / 2-OXOADIPIC ACID / 4-oxalocrotonate decarboxylase NahK
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.571 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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
B: 4-oxalocrotonate decarboxylase NahK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,10320
Polymers57,8682
Non-polymers1,23518
Water11,602644
1
A: 4-oxalocrotonate decarboxylase NahK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,55310
Polymers28,9341
Non-polymers6199
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-oxalocrotonate decarboxylase NahK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,55010
Polymers28,9341
Non-polymers6169
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.328, 44.411, 81.623
Angle α, β, γ (deg.)90.00, 118.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 4-oxalocrotonate decarboxylase NahK


Mass: 28934.121 Da / Num. of mol.: 2 / 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 , 5 types, 662 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-OOG / 2-OXOADIPIC ACID


Mass: 160.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O5
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.18 Å3/Da / Density % sol: 43.57 % / Description: needle-shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: sodium acetate trihydrate, PEG 4000 / PH range: 8.5 - 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.461 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.461 Å / Relative weight: 1
ReflectionResolution: 1.571→40.78 Å / Num. obs: 69868 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 13.25 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 29.704
Reflection shellResolution: 1.571→1.6 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 7.972 / % possible all: 99.8

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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: 1.571→40.78 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1754 3471 4.97 %Random selection
Rwork0.1505 ---
obs0.1518 69848 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.34 Å2
Refinement stepCycle: LAST / Resolution: 1.571→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 80 644 4700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084235
X-RAY DIFFRACTIONf_angle_d1.1525740
X-RAY DIFFRACTIONf_dihedral_angle_d12.9351579
X-RAY DIFFRACTIONf_chiral_restr0.047662
X-RAY DIFFRACTIONf_plane_restr0.004750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5706-1.59210.22911230.17282629X-RAY DIFFRACTION98
1.5921-1.61480.19041280.16442616X-RAY DIFFRACTION100
1.6148-1.63890.19681430.16422646X-RAY DIFFRACTION100
1.6389-1.66450.1811590.15762614X-RAY DIFFRACTION100
1.6645-1.69180.22111310.15322628X-RAY DIFFRACTION100
1.6918-1.7210.22131530.1532664X-RAY DIFFRACTION100
1.721-1.75230.20961380.15672633X-RAY DIFFRACTION100
1.7523-1.7860.19231460.15482659X-RAY DIFFRACTION100
1.786-1.82250.18161500.15432604X-RAY DIFFRACTION100
1.8225-1.86210.19281460.15192653X-RAY DIFFRACTION100
1.8621-1.90540.1771370.15272628X-RAY DIFFRACTION100
1.9054-1.95310.1751400.14342661X-RAY DIFFRACTION100
1.9531-2.00590.18061440.15012641X-RAY DIFFRACTION100
2.0059-2.06490.17741450.14992634X-RAY DIFFRACTION100
2.0649-2.13150.1741440.15122647X-RAY DIFFRACTION100
2.1315-2.20770.17991280.14512704X-RAY DIFFRACTION100
2.2077-2.29610.16691310.15022613X-RAY DIFFRACTION100
2.2961-2.40060.20111650.14882665X-RAY DIFFRACTION100
2.4006-2.52710.17731400.15152659X-RAY DIFFRACTION100
2.5271-2.68540.17861100.15942683X-RAY DIFFRACTION100
2.6854-2.89270.19491290.16052683X-RAY DIFFRACTION100
2.8927-3.18370.18991430.15982701X-RAY DIFFRACTION100
3.1837-3.64420.16151200.14322702X-RAY DIFFRACTION100
3.6442-4.59030.12191320.12972715X-RAY DIFFRACTION100
4.5903-40.79370.16271460.15652695X-RAY DIFFRACTION97

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