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- PDB-4q5o: Crystal structure of EctD from S. alaskensis with 2-oxoglutarate ... -

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Basic information

Entry
Database: PDB / ID: 4q5o
TitleCrystal structure of EctD from S. alaskensis with 2-oxoglutarate and 5-hydroxyectoine
ComponentsEctoine hydroxylase
KeywordsOXIDOREDUCTASE / jelly-roll or cupin fold / ectoine hydroxylase
Function / homology
Function and homology information


ectoine hydroxylase / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding
Similarity search - Function
Ectoine dioxygenase / q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6CS / 2-OXOGLUTARIC ACID / : / Ectoine dioxygenase
Similarity search - Component
Biological speciesSphingopyxis alaskensis RB2256 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsHoeppner, A. / Widderich, N. / Bremer, E. / Smits, S.H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal structure of the ectoine hydroxylase, a snapshot of the active site.
Authors: Hoppner, A. / Widderich, N. / Lenders, M. / Bremer, E. / Smits, S.H.
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif / struct_site
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_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.ptnr1_label_seq_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.ptnr3_label_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ectoine hydroxylase
B: Ectoine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1738
Polymers70,4532
Non-polymers7206
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-15 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.004, 87.076, 94.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ectoine hydroxylase


Mass: 35226.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingopyxis alaskensis RB2256 (bacteria)
Strain: DSM 13593 / LMG 18877 / RB2256 / Gene: Sala_2952 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1GNW5
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-6CS / (4S,5S)-5-HYDROXY-2-METHYL-1,4,5,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID


Mass: 158.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES pH 6.0, 200 mM Ca-acetate, 30% (w/v) PEG 400 , VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 17, 2013
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.64→30 Å / Num. all: 20291 / Num. obs: 20236 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.64→2.74 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MHR

4mhr


Resolution: 2.64→30 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2786 1035 5.12 %random
Rwork0.2063 ---
all0.21 20291 --
obs0.21 20233 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.64→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4396 0 44 29 4469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0214564
X-RAY DIFFRACTIONf_angle_d1.9726232
X-RAY DIFFRACTIONf_dihedral_angle_d15.1811670
X-RAY DIFFRACTIONf_chiral_restr0.081670
X-RAY DIFFRACTIONf_plane_restr0.007832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6401-2.77930.3691490.30212672X-RAY DIFFRACTION100
2.7793-2.95340.35661490.26432684X-RAY DIFFRACTION100
2.9534-3.18140.35351550.24372706X-RAY DIFFRACTION100
3.1814-3.50140.33671440.23092733X-RAY DIFFRACTION100
3.5014-4.00760.25651390.19842746X-RAY DIFFRACTION100
4.0076-5.04770.25831430.16912767X-RAY DIFFRACTION100
5.0477-40.94090.22891560.1922890X-RAY DIFFRACTION100

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