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- PDB-5dqp: EDTA monooxygenase (EmoA) from Chelativorans sp. BNC1 -

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Basic information

Entry
Database: PDB / ID: 5dqp
TitleEDTA monooxygenase (EmoA) from Chelativorans sp. BNC1
ComponentsEDTA monooxygenase
KeywordsOXIDOREDUCTASE / Monooxygenase / Bioremediation / EDTA degradation
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity
Similarity search - Function
Nitrilotriacetate monooxygenase component A/pristinamycin IIA synthase subunit A / : / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesEDTA-degrading bacterium BNC1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.146 Å
AuthorsJun, S.Y. / Youn, B. / Xun, L. / Kang, C. / Lewis, K.M.
CitationJournal: Mol.Microbiol. / Year: 2016
Title: Structural and biochemical characterization of EDTA monooxygenase and its physical interaction with a partner flavin reductase.
Authors: Jun, S.Y. / Lewis, K.M. / Youn, B. / Xun, L. / Kang, C.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EDTA monooxygenase
B: EDTA monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2224
Polymers94,7722
Non-polymers4502
Water10,521584
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-49 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.332, 87.332, 262.704
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-625-

HOH

21A-834-

HOH

31A-901-

HOH

41A-908-

HOH

51A-919-

HOH

61B-559-

HOH

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Components

#1: Protein EDTA monooxygenase


Mass: 47385.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EDTA-degrading bacterium BNC1 (bacteria)
Gene: emoA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9F9T3
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.5, 2% (w/v) PEG 400, and 1.75 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.146→45.02 Å / Num. obs: 56556 / % possible obs: 99.8 % / Redundancy: 10.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.191 / Net I/σ(I): 9.2
Reflection shellResolution: 2.146→2.18 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.194 / Mean I/σ(I) obs: 3.6 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YW1

1yw1


Resolution: 2.146→45.021 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 1989 3.53 %
Rwork0.1899 --
obs0.1915 56296 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.146→45.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6492 0 29 584 7105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096694
X-RAY DIFFRACTIONf_angle_d0.9739117
X-RAY DIFFRACTIONf_dihedral_angle_d17.4174029
X-RAY DIFFRACTIONf_chiral_restr0.056997
X-RAY DIFFRACTIONf_plane_restr0.0071208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1461-2.19980.31231380.23473751X-RAY DIFFRACTION98
2.1998-2.25930.29861380.22923801X-RAY DIFFRACTION100
2.2593-2.32570.27781420.21923859X-RAY DIFFRACTION100
2.3257-2.40080.26921380.20643829X-RAY DIFFRACTION100
2.4008-2.48660.26761410.20853845X-RAY DIFFRACTION100
2.4866-2.58620.23921400.20523848X-RAY DIFFRACTION100
2.5862-2.70380.24041420.20583840X-RAY DIFFRACTION100
2.7038-2.84640.26841410.20313832X-RAY DIFFRACTION99
2.8464-3.02470.25261430.19683871X-RAY DIFFRACTION99
3.0247-3.25820.22031410.19593868X-RAY DIFFRACTION99
3.2582-3.58590.20931430.18073857X-RAY DIFFRACTION99
3.5859-4.10450.20141440.16283907X-RAY DIFFRACTION99
4.1045-5.170.20381430.16053978X-RAY DIFFRACTION99
5.17-45.0310.23781550.19164221X-RAY DIFFRACTION99

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