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- PDB-6g3f: Crystal structure of EDDS lyase in complex with fumarate -

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Basic information

Entry
Database: PDB / ID: 6g3f
TitleCrystal structure of EDDS lyase in complex with fumarate
ComponentsArgininosuccinate lyase
KeywordsLYASE / C-N Lyase / metal chelator / EDDS / tetramer / aspartase fumarase superfamily
Function / homology
Function and homology information


argininosuccinate lyase / argininosuccinate lyase activity / L-arginine biosynthetic process via ornithine / L-arginine biosynthetic process / cytosol
Similarity search - Function
Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarase/aspartase (C-terminal domain) / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like ...Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarase/aspartase (C-terminal domain) / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FUMARIC ACID / DI(HYDROXYETHYL)ETHER / Argininosuccinate lyase
Similarity search - Component
Biological speciesChelativorans sp.
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.222 Å
AuthorsPoddar, H. / Thunnissem, A.M.W.H. / Poelarends, G.J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Research Council242293 Netherlands
CitationJournal: Biochemistry / Year: 2018
Title: Structural Basis for the Catalytic Mechanism of Ethylenediamine- N, N'-disuccinic Acid Lyase, a Carbon-Nitrogen Bond-Forming Enzyme with a Broad Substrate Scope.
Authors: Poddar, H. / de Villiers, J. / Zhang, J. / Puthan Veetil, V. / Raj, H. / Thunnissen, A.W.H. / Poelarends, G.J.
History
DepositionMar 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Argininosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,72310
Polymers55,7581
Non-polymers9659
Water4,666259
1
A: Argininosuccinate lyase
hetero molecules

A: Argininosuccinate lyase
hetero molecules

A: Argininosuccinate lyase
hetero molecules

A: Argininosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,89340
Polymers223,0334
Non-polymers3,86036
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Buried area42260 Å2
ΔGint15 kcal/mol
Surface area59070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.566, 146.017, 152.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-944-

HOH

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Components

#1: Protein Argininosuccinate lyase


Mass: 55758.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chelativorans sp. (strain BNC1) (bacteria)
Strain: BNC1 / Gene: Meso_0564 / Plasmid: pBADN / Production host: Escherichia coli (E. coli) / References: UniProt: Q11KV9
#2: Chemical ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 0.2-0.3 M sodium fumarate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.22→52.7 Å / Num. obs: 39635 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 26
Reflection shellResolution: 2.22→2.27 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 9.5 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G3D

6g3d


Resolution: 2.222→52.637 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.84
RfactorNum. reflection% reflection
Rfree0.1943 1993 5.03 %
Rwork0.1683 --
obs0.1696 39635 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.222→52.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 64 259 4135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033929
X-RAY DIFFRACTIONf_angle_d0.5435305
X-RAY DIFFRACTIONf_dihedral_angle_d13.3572380
X-RAY DIFFRACTIONf_chiral_restr0.037612
X-RAY DIFFRACTIONf_plane_restr0.003686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2221-2.27770.23621470.19992407X-RAY DIFFRACTION90
2.2777-2.33930.22631280.17752712X-RAY DIFFRACTION100
2.3393-2.40810.21631410.17992646X-RAY DIFFRACTION100
2.4081-2.48580.23791710.17312669X-RAY DIFFRACTION100
2.4858-2.57470.20641240.1732734X-RAY DIFFRACTION100
2.5747-2.67780.20761460.16692656X-RAY DIFFRACTION100
2.6778-2.79960.21931440.17312694X-RAY DIFFRACTION100
2.7996-2.94720.22931500.19262713X-RAY DIFFRACTION100
2.9472-3.13180.22111360.19552693X-RAY DIFFRACTION100
3.1318-3.37360.18641360.18832712X-RAY DIFFRACTION100
3.3736-3.7130.18491310.17472726X-RAY DIFFRACTION100
3.713-4.25010.15651270.14942757X-RAY DIFFRACTION100
4.2501-5.35390.15761460.13142733X-RAY DIFFRACTION100
5.3539-52.65220.17821660.1552790X-RAY DIFFRACTION98

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