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- PDB-5j84: Crystal structure of L-arabinonate dehydratase in holo-form -

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Basic information

Entry
Database: PDB / ID: 5j84
TitleCrystal structure of L-arabinonate dehydratase in holo-form
ComponentsDihydroxy-acid dehydratase
KeywordsLYASE / L-arabinonate dehydratase / L-arabonate dehydratase / pentonate dehydratase / 2Fe2S cluster
Function / homology
Function and homology information


L-arabinonate dehydratase / D-fuconate dehydratase / D-fuconate dehydratase activity / L-arabinonate dehydratase activity / galactonate dehydratase / galactonate dehydratase activity / arabinose catabolic process / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
: / 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 / L-arabinonate dehydratase
Similarity search - Component
Biological speciesRhizobium leguminosarum bv. trifolii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: Dihydroxy-acid dehydratase
B: Dihydroxy-acid dehydratase
C: Dihydroxy-acid dehydratase
D: Dihydroxy-acid dehydratase
E: Dihydroxy-acid dehydratase
F: Dihydroxy-acid dehydratase
G: Dihydroxy-acid dehydratase
H: Dihydroxy-acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)512,47324
Polymers510,8728
Non-polymers1,60116
Water31,9051771
1
A: Dihydroxy-acid dehydratase
B: Dihydroxy-acid dehydratase
C: Dihydroxy-acid dehydratase
D: Dihydroxy-acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,23612
Polymers255,4364
Non-polymers8018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23430 Å2
ΔGint-192 kcal/mol
Surface area63270 Å2
MethodPISA
2
E: Dihydroxy-acid dehydratase
F: Dihydroxy-acid dehydratase
G: Dihydroxy-acid dehydratase
H: Dihydroxy-acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,23612
Polymers255,4364
Non-polymers8018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23570 Å2
ΔGint-194 kcal/mol
Surface area63550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.070, 208.610, 147.090
Angle α, β, γ (deg.)90.00, 90.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dihydroxy-acid dehydratase


Mass: 63858.938 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Gram-negative bacteria
Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (strain WSM2304) (bacteria)
Strain: WSM2304 / Gene: Rleg2_2909 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5ZZ34, dihydroxy-acid dehydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8
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)
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 8
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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1771 / 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: 3.2 Å3/Da / Density % sol: 62 % / Description: 3D-Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 4 M Sodium formate, 0.1 M MES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.97957 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 246940 / % possible obs: 99.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 43 Å2 / CC1/2: 0.995 / Rsym value: 0.091 / Net I/σ(I): 12.3
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GP4

2gp4


Resolution: 2.4→39.889 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.35
RfactorNum. reflection% reflection
Rfree0.1853 12487 5.06 %
Rwork0.1556 --
obs0.155 246940 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→39.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34792 0 40 1771 36603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00635581
X-RAY DIFFRACTIONf_angle_d0.80748230
X-RAY DIFFRACTIONf_dihedral_angle_d11.65413144
X-RAY DIFFRACTIONf_chiral_restr0.0315344
X-RAY DIFFRACTIONf_plane_restr0.0036304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.44150.3186080.253211536X-RAY DIFFRACTION93
2.4415-2.48590.28116190.239611776X-RAY DIFFRACTION95
2.4859-2.53370.28196180.232211739X-RAY DIFFRACTION95
2.5337-2.58540.25136200.217411783X-RAY DIFFRACTION95
2.5854-2.64160.27466170.219411708X-RAY DIFFRACTION95
2.6416-2.7030.25236170.217211733X-RAY DIFFRACTION95
2.703-2.77060.24446190.199911749X-RAY DIFFRACTION95
2.7706-2.84550.22076180.191411746X-RAY DIFFRACTION95
2.8455-2.92920.22246180.183911754X-RAY DIFFRACTION95
2.9292-3.02370.23086180.180311737X-RAY DIFFRACTION95
3.0237-3.13170.20246210.169211789X-RAY DIFFRACTION95
3.1317-3.25710.19436160.167111704X-RAY DIFFRACTION95
3.2571-3.40520.18676170.157311733X-RAY DIFFRACTION94
3.4052-3.58470.18176180.145211730X-RAY DIFFRACTION94
3.5847-3.80910.16056140.135311678X-RAY DIFFRACTION94
3.8091-4.10290.14376180.123511739X-RAY DIFFRACTION94
4.1029-4.51530.13396130.11211651X-RAY DIFFRACTION94
4.5153-5.16740.1326180.110811742X-RAY DIFFRACTION94
5.1674-6.50580.13766200.124711767X-RAY DIFFRACTION94
6.5058-39.6510.1576200.130411780X-RAY DIFFRACTION94

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