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- PDB-5j85: Ser480Ala mutant of L-arabinonate dehydratase -

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Basic information

Entry
Database: PDB / ID: 5j85
TitleSer480Ala mutant of L-arabinonate dehydratase
ComponentsDihydroxyacid dehydratase/phosphogluconate dehydratase
KeywordsLYASE / L-arabinonate dehydratase / L-arabonate dehydratase / pentonate dehydratase / 2Fe2S cluster
Function / homology
Function and homology information


hydro-lyase activity / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
: / : / Dihydroxy-acid/6-phosphogluconate dehydratase C-terminal / Dihydroxy-acid/6-phosphogluconate dehydratase / IlvD/EDD, N-terminal domain / Dihydroxy-acid dehydratase, C-terminal / Dihydroxy-acid/6-phosphogluconate dehydratase N-terminal
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Dihydroxyacid dehydratase/phosphogluconate dehydratase
Similarity search - Component
Biological speciesRhizobium leguminosarum bv. trifolii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRahman, M.M. / Rouvinen, J. / Hakulinen, N.
Funding support Finland, 2items
OrganizationGrant numberCountry
Finnish Academy256937 Finland
Finnish Academy263931 Finland
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: The Crystal Structure of a Bacterial l-Arabinonate Dehydratase Contains a [2Fe-2S] Cluster.
Authors: Rahman, M.M. / Andberg, M. / Thangaraj, S.K. / Parkkinen, T. / Penttila, M. / Janis, J. / Koivula, A. / Rouvinen, J. / Hakulinen, N.
History
DepositionApr 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 10, 2024Group: 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroxyacid dehydratase/phosphogluconate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0433
Polymers63,8431
Non-polymers2002
Water3,297183
1
A: Dihydroxyacid dehydratase/phosphogluconate dehydratase
hetero molecules

A: Dihydroxyacid dehydratase/phosphogluconate dehydratase
hetero molecules

A: Dihydroxyacid dehydratase/phosphogluconate dehydratase
hetero molecules

A: Dihydroxyacid dehydratase/phosphogluconate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,17212
Polymers255,3724
Non-polymers8018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation28_544x,-y-1/2,-z-1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
Buried area23890 Å2
ΔGint-200 kcal/mol
Surface area66650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)318.440, 318.440, 318.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-878-

HOH

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Components

#1: Protein Dihydroxyacid dehydratase/phosphogluconate dehydratase


Mass: 63842.938 Da / Num. of mol.: 1 / Mutation: S480A
Source method: isolated from a genetically manipulated source
Details: Gram-negative bacteria
Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (bacteria)
Gene: Rleg9DRAFT_6269 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I9XDU6
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Mutation: S480A
Source method: isolated from a genetically manipulated source
Formula: Fe2S2 / Details: Gram-negative bacteria
Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (bacteria)
Gene: 6981653 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: L-arabinonate dehydratase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Mutation: S480A
Source method: isolated from a genetically manipulated source
Formula: Mg / Details: Gram-negative bacteria
Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (bacteria)
Gene: 6981653 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: L-arabinonate dehydratase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 5.3 Å3/Da / Density % sol: 77 % / Description: cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M sodium chloride, 0.1 M BTP pH 9.0, 5 mM magnesium chloride, 17% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 42880 / % possible obs: 99.8 % / Redundancy: 9.7 % / Biso Wilson estimate: 74 Å2 / CC1/2: 0.998 / Rsym value: 0.082 / Net I/σ(I): 17
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 2.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GP4

2gp4


Resolution: 2.6→38.904 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2027 2143 5 %
Rwork0.1793 --
obs0.1805 42876 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→38.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 5 183 4545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094476
X-RAY DIFFRACTIONf_angle_d0.9126057
X-RAY DIFFRACTIONf_dihedral_angle_d3.3353716
X-RAY DIFFRACTIONf_chiral_restr0.051671
X-RAY DIFFRACTIONf_plane_restr0.005795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.66050.41131390.41332640X-RAY DIFFRACTION99
2.6605-2.7270.36731390.30242659X-RAY DIFFRACTION100
2.727-2.80070.31011410.27292668X-RAY DIFFRACTION100
2.8007-2.88310.32591410.24832673X-RAY DIFFRACTION100
2.8831-2.97620.27721400.24542670X-RAY DIFFRACTION100
2.9762-3.08250.27941410.22932673X-RAY DIFFRACTION100
3.0825-3.20590.29521410.22492690X-RAY DIFFRACTION100
3.2059-3.35170.26651420.21742698X-RAY DIFFRACTION100
3.3517-3.52830.24231420.19912685X-RAY DIFFRACTION100
3.5283-3.74920.20641420.18522708X-RAY DIFFRACTION100
3.7492-4.03840.19611430.15632712X-RAY DIFFRACTION100
4.0384-4.44430.1551440.14452738X-RAY DIFFRACTION100
4.4443-5.08610.14241450.13472752X-RAY DIFFRACTION100
5.0861-6.40340.18411470.16952804X-RAY DIFFRACTION100
6.4034-38.9080.16761560.16332963X-RAY DIFFRACTION99

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