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- PDB-4nmi: Crystal Structure of the Apo ectoine hydroxylase ECTD from Saliba... -

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Basic information

Entry
Database: PDB / ID: 4nmi
TitleCrystal Structure of the Apo ectoine hydroxylase ECTD from Salibacillus salexigens
ComponentsEctD
KeywordsOXIDOREDUCTASE / jelly-roll or cupin fold / metal ion binding / Iron
Function / homology
Function and homology information


ectoine hydroxylase / ectoine catabolic process / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding
Similarity search - Function
Ectoine dioxygenase / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesVirgibacillus salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsWidderich, N. / Hoeppner, A. / Smits, S.H. / Bremer, E.
CitationJournal: Plos One / Year: 2014
Title: Biochemical properties of ectoine hydroxylases from extremophiles and their wider taxonomic distribution among microorganisms.
Authors: Widderich, N. / Hoppner, A. / Pittelkow, M. / Heider, J. / Smits, S.H. / Bremer, E.
History
DepositionNov 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EctD


Theoretical massNumber of molelcules
Total (without water)35,6521
Polymers35,6521
Non-polymers00
Water6,287349
1
A: EctD

A: EctD


Theoretical massNumber of molelcules
Total (without water)71,3042
Polymers71,3042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area1960 Å2
ΔGint-15 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.897, 102.897, 159.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

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Components

#1: Protein EctD


Mass: 35651.836 Da / Num. of mol.: 1 / Fragment: ectoine hydroxylase / Source method: isolated from a natural source / Source: (natural) Virgibacillus salexigens (bacteria)
References: UniProt: Q2TDY4, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 3.42 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM MES pH 5.0 and 1.2 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.92 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 14, 2013
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 40025 / Num. obs: 37155 / % possible obs: 92.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.78→1.826 Å / % possible all: 90.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.798 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.084 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19973 2448 5.1 %RANDOM
Rwork0.17159 ---
all0.1716 45919 --
obs0.17302 45956 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.955 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.21 Å20 Å2
2--0.21 Å20 Å2
3----0.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.03 Å
Luzzati d res low-1.8 Å
Luzzati sigma a0.18 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 1.78→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 0 349 2613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192316
X-RAY DIFFRACTIONr_bond_other_d0.0020.022159
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.9523130
X-RAY DIFFRACTIONr_angle_other_deg0.97834982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5295278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03324.426122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40415404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6741516
X-RAY DIFFRACTIONr_chiral_restr0.1270.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212642
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02546
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 196 -
Rwork0.319 3300 -
obs--99.35 %

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