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- PDB-5d2j: 4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - compl... -

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Basic information

Entry
Database: PDB / ID: 5d2j
Title4-oxalocrotonate decarboxylase from Pseudomonas putida G7 - complexed with magnesium and adipate
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
hexanedioic acid / ACETATE ION / 4-oxalocrotonate decarboxylase NahK
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.718 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_asym_id / _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_asym_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)58,51613
Polymers57,8682
Non-polymers64711
Water9,206511
1
A: 4-oxalocrotonate decarboxylase NahK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2536
Polymers28,9341
Non-polymers3195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-oxalocrotonate decarboxylase NahK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2637
Polymers28,9341
Non-polymers3296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.774, 44.547, 81.253
Angle α, β, γ (deg.)90.00, 118.76, 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, 522 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-0L1 / hexanedioic acid / Adipic acid


Mass: 146.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.16 Å3/Da / Density % sol: 43.05 % / 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: 1.459 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: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.718→40.595 Å / Num. obs: 51584 / % possible obs: 97.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 17.76 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.36
Reflection shellResolution: 1.718→1.76 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.008 / % possible all: 80.6

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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: 1.718→40.595 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 2531 4.91 %Random selection
Rwork0.1538 ---
obs0.1556 51551 97.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.15 Å2
Refinement stepCycle: LAST / Resolution: 1.718→40.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3967 0 41 511 4519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064105
X-RAY DIFFRACTIONf_angle_d1.0625570
X-RAY DIFFRACTIONf_dihedral_angle_d12.9531506
X-RAY DIFFRACTIONf_chiral_restr0.076648
X-RAY DIFFRACTIONf_plane_restr0.004728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7182-1.75130.24891060.20752139X-RAY DIFFRACTION78
1.7513-1.7870.24681210.19372369X-RAY DIFFRACTION85
1.787-1.82590.25171460.19582570X-RAY DIFFRACTION93
1.8259-1.86830.26981480.19562658X-RAY DIFFRACTION96
1.8683-1.91510.28171450.18412782X-RAY DIFFRACTION99
1.9151-1.96680.19161420.16422750X-RAY DIFFRACTION99
1.9668-2.02470.18771430.15912798X-RAY DIFFRACTION100
2.0247-2.09010.21861630.15122749X-RAY DIFFRACTION100
2.0901-2.16480.15711450.14672792X-RAY DIFFRACTION100
2.1648-2.25140.17811390.14752797X-RAY DIFFRACTION100
2.2514-2.35390.16761560.1452757X-RAY DIFFRACTION100
2.3539-2.4780.21471540.15512829X-RAY DIFFRACTION100
2.478-2.63320.20671240.15862820X-RAY DIFFRACTION100
2.6332-2.83650.19871340.16412800X-RAY DIFFRACTION100
2.8365-3.12180.1911460.16422821X-RAY DIFFRACTION100
3.1218-3.57330.17451250.14772850X-RAY DIFFRACTION100
3.5733-4.50110.15091350.12722846X-RAY DIFFRACTION100
4.5011-40.60620.18641590.14842893X-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)
11.4945-0.37770.52091.9058-0.40662.0965-0.0324-0.2306-0.06330.20010.04890.14750.0006-0.16730.0050.1094-0.00770.00510.12830.01060.1153-15.740814.84118.5462
21.7416-0.63580.23881.4212-0.07231.221-0.0044-0.0197-0.11030.0277-0.00950.04730.0450.033-0.00520.0781-0.02430.01930.10260.00360.1112-21.800514.82796.0664
30.7952-0.21030.05531.41890.52661.019-0.03660.0441-0.1208-0.0690.03360.06710.00410.00910.01530.0764-0.00130.02450.10820.00060.1327-29.100613.98690.5764
41.7457-0.30940.48311.8639-0.40594.51670.0116-0.2072-0.02510.08620.00360.20280.0068-0.41360.00330.1134-0.02850.00940.150.0180.1733-2.6477-9.278831.5077
51.69011.24150.12991.97650.70951.8350.05-0.06560.00280.04940.02070.09470.0796-0.0528-0.03990.08180.0113-0.01150.09580.01860.10189.2836-4.797928.834
61.43490.05260.56170.9453-0.03721.04470.02550.07030.0099-0.00920.00860.050.0095-0.0268-0.0410.1150.0170.01540.06620.0020.090111.7743-0.08222.223
71.93720.07650.74671.81460.61672.8869-0.04880.02530.182-0.04370.022-0.2063-0.08980.07110.03860.1368-0.0170.0470.09530.00710.112719.125612.116515.5627
80.9787-0.29810.86820.2038-0.27171.5373-0.01310.0190.00210.014-0.00240.0378-0.05550.03710.00240.1299-0.00150.00930.0834-0.01140.116515.88731.191525.7821
95.10091.02422.64421.31940.50033.1657-0.08910.34120.1097-0.0880.07090.0211-0.24780.25050.07080.1370.01030.01950.1574-0.00390.080614.03936.7676.9845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 171 )
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 264 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 38 )
5X-RAY DIFFRACTION5chain 'B' and (resid 39 through 76 )
6X-RAY DIFFRACTION6chain 'B' and (resid 77 through 170 )
7X-RAY DIFFRACTION7chain 'B' and (resid 171 through 207 )
8X-RAY DIFFRACTION8chain 'B' and (resid 208 through 247 )
9X-RAY DIFFRACTION9chain 'B' and (resid 248 through 264 )

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