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- PDB-3emr: Crystal Structure Analysis of the ectoine hydroxylase ECTD from S... -

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Basic information

Entry
Database: PDB / ID: 3emr
TitleCrystal Structure Analysis of the ectoine hydroxylase ECTD from Salibacillus salexigens
ComponentsEctD
KeywordsOXIDOREDUCTASE / double stranded beta helix
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
: / Ectoine dioxygenase
Similarity search - Component
Biological speciesVirgibacillus salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsReuter, K. / Heine, A.
CitationJournal: Plos One / Year: 2010
Title: Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II) and 2-oxoglutarate-dependent dioxygenase EctD
Authors: Reuter, K. / Pittelkow, M. / Bursy, J. / Heine, A. / Craan, T. / Bremer, E.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_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

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Assembly

Deposited unit
A: EctD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6048
Polymers35,9801
Non-polymers6247
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: EctD
hetero molecules

A: EctD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,20916
Polymers71,9602
Non-polymers1,24914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area4800 Å2
ΔGint-134 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.790, 102.790, 159.070
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-852-

HOH

21A-892-

HOH

DetailsECTD HAS CLEARLY BEEN SHOWN BY SIZE EXCLUSION CHROMATOGRAPHY TO BE A MONOMER IN SOLUTION (BURSY ET AL. 2007, J. BIOL. CHEM. 282, PP31147-31155), AGAINST PISA'S SUGGESTION, A HOMODIMER.

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Components

#1: Protein EctD / Ectoine Hydroxylase


Mass: 35980.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cell / Source: (gene. exp.) Virgibacillus salexigens (bacteria) / Strain: DSM-11483 / Gene: ectD / Plasmid: pASK-IBA3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
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: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.0M ammonium sulfate, 0.1M sodium fluoride, 2mM TCEP, 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.210.9081
SYNCHROTRONBESSY 14.220.90810,0.97971,0.97997
Detector
TypeIDDetectorDateDetails
MAR CCD 165 mm1CCDJan 24, 2006monochromator
MAR CCD 165 mm2CCDJan 24, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1KMC-2 monochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.90811
20.979711
30.979971
ReflectionResolution: 1.85→50 Å / Num. all: 43040 / Num. obs: 43040 / % possible obs: 99.9 % / Redundancy: 14.6 % / Rsym value: 0.067 / Net I/σ(I): 34.1
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 2095 / Rsym value: 0.437 / % possible all: 100

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Processing

Software
NameClassification
MAR345data collection
SHELXDphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.85→10 Å / Num. parameters: 9863 / Num. restraintsaints: 9313 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 2061 -RANDOM
Rwork0.1924 ---
all0.1934 41763 --
obs-39702 97.9 %-
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 2071 / Occupancy sum non hydrogen: 2421.1
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 33 197 2429
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0237
X-RAY DIFFRACTIONs_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.016
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0

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