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- PDB-2z9h: Ethanolamine utilization protein, EutN -

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Basic information

Entry
Database: PDB / ID: 2z9h
TitleEthanolamine utilization protein, EutN
ComponentsEthanolamine utilization protein eutN
KeywordsSTRUCTURAL PROTEIN / hexamer
Function / homology
Function and homology information


ethanolamine catabolic process / protein hexamerization / DNA damage response / identical protein binding
Similarity search - Function
EutN/Ccml / Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Ethanolamine catabolic microcompartment shell protein EutN
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.71 Å
AuthorsTanaka, S. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: To be Published
Title: The crystal structure of ethanolamine utilization protein EutN from E. coli
Authors: Tanaka, S. / Sawaya, M.R. / Kerfeld, C.A. / Yeates, T.O.
History
DepositionSep 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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: Ethanolamine utilization protein eutN
B: Ethanolamine utilization protein eutN
C: Ethanolamine utilization protein eutN
D: Ethanolamine utilization protein eutN
E: Ethanolamine utilization protein eutN
F: Ethanolamine utilization protein eutN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,74011
Polymers66,2326
Non-polymers5085
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.281, 66.540, 72.004
Angle α, β, γ (deg.)90.000, 119.250, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31A
41D
51A
61D
12B
22E
13C
23F

NCS domain segments:

Refine code: 3

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETMETMETAA1 - 291 - 29
211METMETMETMETDD1 - 291 - 29
321GLNGLNVALVALAA39 - 8539 - 85
421GLNGLNVALVALDD39 - 8539 - 85
531ILEILELYSLYSAA92 - 9592 - 95
631ILEILELYSLYSDD92 - 9592 - 95
112METMETLYSLYSBB1 - 951 - 95
212METMETLYSLYSEE1 - 951 - 95
113METMETLYSLYSCC1 - 951 - 95
213METMETLYSLYSFF1 - 951 - 95

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Ethanolamine utilization protein eutN


Mass: 11038.621 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: eutN, cchB / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: P0AEJ8
#2: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1M Bis-Tris, 0.2M ammonium acetate, 50% MPD, pH5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→80 Å / Num. obs: 15586 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.103 / Χ2: 1.092 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.82.30.49414770.988193.5
2.8-2.912.30.43715251.031196.3
2.91-3.042.40.3115660.964197.1
3.04-3.22.40.24115481.174197.5
3.2-3.42.40.16315511.236197.1
3.4-3.662.40.11315671.069197.9
3.66-4.032.40.0915721.116197.8
4.03-4.622.40.07815701.158197.5
4.62-5.822.40.0715971.138198.7
5.82-802.30.05916131.025196.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å62.82 Å
Translation4 Å62.82 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HD3

2hd3


Resolution: 2.71→19.98 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.893 / SU B: 36.655 / SU ML: 0.358 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.302 704 5.1 %RANDOM
Rwork0.243 ---
obs0.246 13732 85.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.709 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.03 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.71→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4029 0 33 21 4083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214112
X-RAY DIFFRACTIONr_bond_other_d0.0010.022589
X-RAY DIFFRACTIONr_angle_refined_deg0.951.9575579
X-RAY DIFFRACTIONr_angle_other_deg0.78136437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3475543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.8626150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52815692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4061510
X-RAY DIFFRACTIONr_chiral_restr0.0570.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024537
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
X-RAY DIFFRACTIONr_nbd_refined0.1870.2864
X-RAY DIFFRACTIONr_nbd_other0.1820.22728
X-RAY DIFFRACTIONr_nbtor_refined0.1570.21954
X-RAY DIFFRACTIONr_nbtor_other0.0820.22317
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1280.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.25
X-RAY DIFFRACTIONr_mcbond_it1.61523460
X-RAY DIFFRACTIONr_mcbond_other0.22321145
X-RAY DIFFRACTIONr_mcangle_it1.84734346
X-RAY DIFFRACTIONr_scbond_it0.78321511
X-RAY DIFFRACTIONr_scangle_it1.09831233
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A471TIGHT POSITIONAL0.020.05
1A504LOOSE POSITIONAL0.565
1A471TIGHT THERMAL0.040.5
1A504LOOSE THERMAL0.6610
2B555TIGHT POSITIONAL0.020.05
2B585LOOSE POSITIONAL0.65
2B555TIGHT THERMAL0.040.5
2B585LOOSE THERMAL0.5710
3C478TIGHT POSITIONAL0.020.05
3C495LOOSE POSITIONAL0.625
3C478TIGHT THERMAL0.040.5
3C495LOOSE THERMAL0.7510
LS refinement shellResolution: 2.712→2.781 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.583 15 -
Rwork0.354 329 -
all-344 -
obs--29.45 %
Refinement TLS params.Method: refined / Origin x: -3.9432 Å / Origin y: 6.3173 Å / Origin z: 19.1309 Å
111213212223313233
T0.2001 Å20.009 Å20.0011 Å2-0.0999 Å2-0.0051 Å2--0.1913 Å2
L1.1528 °20.0885 °2-0.2668 °2-0.0088 °20.0372 °2--1.6895 °2
S-0.0354 Å °-0.4181 Å °-0.0168 Å °0.024 Å °0.002 Å °0.0057 Å °0.03 Å °0.0083 Å °0.0334 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 951 - 95
2X-RAY DIFFRACTION1BB1 - 951 - 95
3X-RAY DIFFRACTION1CC1 - 951 - 95
4X-RAY DIFFRACTION1DD1 - 951 - 95
5X-RAY DIFFRACTION1EE1 - 951 - 95
6X-RAY DIFFRACTION1FF1 - 951 - 95

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