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- PDB-5d2i: 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - compl... -

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Basic information

Entry
Database: PDB / ID: 5d2i
Title4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - complexed with calcium and acetate
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: 1.78 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.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 / _struct_conn.ptnr2_symmetry

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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)58,84519
Polymers57,8682
Non-polymers97717
Water10,881604
1
A: 4-oxalocrotonate decarboxylase NahK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,44310
Polymers28,9341
Non-polymers5099
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-oxalocrotonate decarboxylase NahK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4039
Polymers28,9341
Non-polymers4698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.494, 43.750, 79.495
Angle α, β, γ (deg.)90.00, 118.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.05 Å3/Da / Density % sol: 40.06 % / 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: D03B-MX1 / Wavelength: 1.43 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
ReflectionResolution: 1.78→26.68 Å / Num. obs: 45445 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 16.63 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.293
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.981 / % possible all: 100

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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: 1.78→26.68 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 2227 4.9 %Random selection
Rwork0.1457 ---
obs0.1476 45430 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.93 Å2
Refinement stepCycle: LAST / Resolution: 1.78→26.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 59 604 4600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084091
X-RAY DIFFRACTIONf_angle_d1.1755540
X-RAY DIFFRACTIONf_dihedral_angle_d12.61495
X-RAY DIFFRACTIONf_chiral_restr0.071643
X-RAY DIFFRACTIONf_plane_restr0.004723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.81870.29961470.2692677X-RAY DIFFRACTION100
1.8187-1.8610.2761450.1892643X-RAY DIFFRACTION100
1.861-1.90750.20911370.17112701X-RAY DIFFRACTION100
1.9075-1.95910.23021430.17622660X-RAY DIFFRACTION100
1.9591-2.01670.2211530.14632689X-RAY DIFFRACTION100
2.0167-2.08180.1831400.14292683X-RAY DIFFRACTION100
2.0818-2.15620.17831310.1352679X-RAY DIFFRACTION100
2.1562-2.24250.18891370.1382666X-RAY DIFFRACTION100
2.2425-2.34450.17831530.13642682X-RAY DIFFRACTION100
2.3445-2.4680.19151460.14212689X-RAY DIFFRACTION100
2.468-2.62250.19021130.15072731X-RAY DIFFRACTION100
2.6225-2.82480.17811320.14972699X-RAY DIFFRACTION100
2.8248-3.10860.20521430.15072721X-RAY DIFFRACTION100
3.1086-3.55760.16321240.1342726X-RAY DIFFRACTION100
3.5576-4.47870.1331290.12182754X-RAY DIFFRACTION100
4.4787-26.68340.1851540.14652803X-RAY DIFFRACTION100
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)
11.672-0.64920.18692.1544-0.58266.55610.1292-0.3484-0.11390.13050.03650.22250.2883-0.2713-0.06090.127-0.06080.00780.17850.03290.15170.004-12.549531.7436
21.4284-0.16590.80861.79350.1376.8133-0.0807-0.38260.14690.1457-0.11670.468-0.1905-0.9733-0.04550.1206-0.02150.03180.2869-0.03110.2069-5.0985-5.080430.4394
31.90041.36140.3052.15390.44072.21550.0826-0.1294-0.02890.0716-0.03210.13830.1268-0.0946-0.04140.07970.0111-0.01160.08970.01970.09589.4636-5.154228.3833
41.6227-0.01290.66890.8746-0.14321.07840.05250.01160.04150.0463-0.0258-0.02580.03640.0269-0.02330.10660.01070.01220.0622-0.00280.076315.81660.086221.1604
50.61690.53730.87472.3907-0.58662.3791-0.0686-0.15280.07560.16240.01330.2641-0.2008-0.32480.01960.10350.036-0.00660.111-0.01220.11452.7341-0.40823.6081
60.9416-0.20760.65511.1261-0.18522.0057-0.08940.07580.16670.00850.0342-0.2139-0.13830.12210.12210.1434-0.01250.00070.10440.00090.143818.924212.136115.5476
70.7433-0.34040.70440.5177-0.39091.31880.00210.0021-0.01260.05150.01050.0058-0.03320.0054-0.01350.1210.0020.00120.0908-0.01120.110115.93871.067925.3016
86.26154.40135.38614.14612.8365.5886-0.20030.50910.1233-0.13780.1649-0.0315-0.25770.32050.11950.11940.01620.01310.12340.00320.095513.89136.86746.9526
92.0947-0.2903-1.16823.02131.64994.2705-0.0313-0.3517-0.09350.4938-0.02550.02430.07690.01120.06350.1890.0352-0.0180.18410.03050.1018-10.842612.034822.4156
103.0368-0.7640.34111.61280.16053.1942-0.1066-0.3001-0.03690.20390.0270.15190.1632-0.21040.06780.15080.01860.00690.1054-0.00710.0881-19.929617.277514.665
111.4625-0.49380.21131.31880.03541.242-0.0004-0.0487-0.05380.0530.00440.05520.03820.0259-0.01440.0679-0.01780.01350.08130.00370.0907-21.518515.48815.5442
121.2764-0.5237-0.00621.67180.55551.0362-0.01870.0464-0.0865-0.01320.00320.16250.021-0.00310.03080.0759-0.00310.01530.08740.00930.124-28.562313.86180.5524
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 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 144 )
5X-RAY DIFFRACTION5chain 'A' and (resid 145 through 171 )
6X-RAY DIFFRACTION6chain 'A' and (resid 172 through 207 )
7X-RAY DIFFRACTION7chain 'A' and (resid 208 through 247 )
8X-RAY DIFFRACTION8chain 'A' and (resid 248 through 264 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 38 )
10X-RAY DIFFRACTION10chain 'B' and (resid 39 through 81 )
11X-RAY DIFFRACTION11chain 'B' and (resid 82 through 170 )
12X-RAY DIFFRACTION12chain 'B' and (resid 171 through 264 )

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