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- PDB-2pyt: Crystal structure of a putative ethanolamine utilization protein ... -

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Basic information

Entry
Database: PDB / ID: 2pyt
TitleCrystal structure of a putative ethanolamine utilization protein q (eutq, stm2468) from salmonella typhimurium lt2 at 1.90 A resolution
ComponentsEthanolamine utilization protein eutQ
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


acetate kinase / ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / acetate kinase activity / generation of precursor metabolites and energy / ATP binding
Similarity search - Function
Acetate kinase EutQ / Ethanolamine utilisation protein EutQ / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Ethanolamine utilization protein eutQ (16421009) from Salmonella typhimurium LT2 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). EBI/PISA ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT EXPRESSED PROTEIN SEQUENCE 98-229 WITH A PURIFICATION TAG ... SEQUENCE THE CONSTRUCT EXPRESSED PROTEIN SEQUENCE 98-229 WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ethanolamine utilization protein eutQ
B: Ethanolamine utilization protein eutQ


Theoretical massNumber of molelcules
Total (without water)29,5512
Polymers29,5512
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-33 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.151, 39.043, 44.923
Angle α, β, γ (deg.)109.990, 104.790, 95.380
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ethanolamine utilization protein eutQ


Mass: 14775.608 Da / Num. of mol.: 2 / Fragment: Residues 98-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria) / Species: Salmonella typhimurium / Strain: LT2, SGSC1412 / Gene: 16421009, eutQ, STM2468 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9ZFV5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: NANODROP, 2.4M (NH4)2SO4, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97901, 0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 3, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979011
30.979291
ReflectionResolution: 1.9→28.49 Å / Num. obs: 17651 / % possible obs: 97 % / Redundancy: 2 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 3.4
Reflection shell

Redundancy: 2 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.950.3350.8257513130.33596.3
1.95-20.2322.8246812530.23296.1
2-2.060.1993.2239312210.19996.1
2.06-2.120.2330.5236412030.23396.8
2.12-2.190.1664225311470.16696.5
2.19-2.270.1661.4222211330.16696.8
2.27-2.360.1314.8214710900.13196.8
2.36-2.450.1175.4204510390.11796.8
2.45-2.560.1225.3201110210.12297.3
2.56-2.690.1182.218689500.11897.3
2.69-2.830.0915.718039170.09197.7
2.83-30.0827.117468820.08297.1
3-3.210.0835.415838080.08397.6
3.21-3.470.0736.914947630.07398.2
3.47-3.80.0627.613556890.06298
3.8-4.250.068.412576400.0697.7
4.25-4.910.0568.510915540.05697.9
4.91-6.010.06989244700.06998.7
6.01-8.50.07877323720.07898.2
8.5-28.490.0925.13631860.09292.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.9→28.49 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.218 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.156
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. RESIDUES 98-99, 228-229 IN CHAIN A AND 98-102, 226-229 IN CHAIN B ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. RAMACHANDRAN OUTLIER RESIDUE ASN 162 IS SUPPORTED BY THE DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 895 5.1 %RANDOM
Rwork0.173 ---
obs0.175 17650 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.245 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0.93 Å2-2.29 Å2
2---1.2 Å20.02 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 0 185 2098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221997
X-RAY DIFFRACTIONr_bond_other_d0.0020.021315
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9322721
X-RAY DIFFRACTIONr_angle_other_deg1.06433216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2915263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63624.47185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65915309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.747156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022274
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02421
X-RAY DIFFRACTIONr_nbd_refined0.1660.2271
X-RAY DIFFRACTIONr_nbd_other0.1770.21313
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2935
X-RAY DIFFRACTIONr_nbtor_other0.0810.21094
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2146
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.210
X-RAY DIFFRACTIONr_mcbond_it2.4231363
X-RAY DIFFRACTIONr_mcbond_other0.5383525
X-RAY DIFFRACTIONr_mcangle_it3.08652026
X-RAY DIFFRACTIONr_scbond_it5.5658838
X-RAY DIFFRACTIONr_scangle_it7.08211688
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 65 -
Rwork0.248 1244 -
obs-1309 96.18 %

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