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- PDB-3n2x: Crystal structure of YagE, a prophage protein belonging to the di... -

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Basic information

Entry
Database: PDB / ID: 3n2x
TitleCrystal structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12 in complex with pyruvate
ComponentsUncharacterized protein yagE
KeywordsLYASE / TIM Barrel / Protein-Ligand Complex / Aldolase
Function / homology
Function and homology information


2-dehydro-3-deoxy-D-pentonate aldolase / aldonic acid catabolic process / 2-dehydro-3-deoxy-D-pentonate aldolase activity / 2-dehydro-3-deoxy-D-gluconate aldolase / 2-dehydro-3-deoxy-D-gluconate aldolase activity / identical protein binding / cytosol
Similarity search - Function
Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBhaskar, V. / Kumar, P.M. / Manicka, S. / Krishnaswamy, S.
CitationJournal: Proteins / Year: 2011
Title: Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis.
Authors: Bhaskar, V. / Kumar, M. / Manicka, S. / Tripathi, S. / Venkatraman, A. / Krishnaswamy, S.
History
DepositionMay 19, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0May 30, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_mod_residue.auth_comp_id / _pdbx_struct_mod_residue.label_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_validate_close_contact.auth_comp_id_1 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Nov 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_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein yagE
B: Uncharacterized protein yagE
C: Uncharacterized protein yagE
D: Uncharacterized protein yagE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0048
Polymers128,7554
Non-polymers2484
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-50 kcal/mol
Surface area38080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.130, 153.550, 55.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-380-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
31B
41C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 3 / Auth seq-ID: 12 - 309 / Label seq-ID: 1 - 298

Dom-IDAuth asym-IDLabel asym-ID
1DD
2AA
3BB
4CC

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Components

#1: Protein
Uncharacterized protein yagE / A CP4-6 Prophage Protein


Mass: 32188.811 Da / Num. of mol.: 4 / Fragment: UNP residues 12-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0268, JW0261, yagE / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P75682
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5
Details: 100mM HEPES pH 6.5, 200mM MgCl2, 25% PEG 3350, Microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.973 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.2→48.975 Å / Num. obs: 62107 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.397 Å2 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.11 / Net I/σ(I): 16.93
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.250.2650.3395.930893454643620.3796
2.25-2.310.2230.2976.933011448844630.3299.4
2.31-2.380.2030.2677.731943429342800.2999.7
2.38-2.460.1790.2338.731002420041750.2599.4
2.46-2.540.1630.219.630377411941000.2299.5
2.54-2.620.1390.1811129193393939270.1999.7
2.62-2.720.1330.17211.428195381038000.1999.7
2.72-2.840.1160.15612.527201368336690.1799.6
2.84-2.960.1050.13714.126064354135250.1599.5
2.96-3.110.0830.10717.224930339733870.1299.7
3.11-3.270.070.09119.523741323932250.199.6
3.27-3.470.0540.0722422334306530450.0899.3
3.47-3.710.0450.06227.420979288728790.0799.7
3.71-4.010.0390.05330.119371268026640.0699.4
4.01-4.390.0330.04833.517779248424730.0599.6
4.39-4.910.0320.04434.716150226822600.0599.6
4.91-5.670.0420.04930.414261202720190.0599.6
5.67-6.940.0480.05128.912125173617250.0599.4
6.94-9.820.0320.03636.69087135413370.0498.7
9.820.0290.03137.149418167920.0397.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V8Z

2v8z


Resolution: 2.2→48.975 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.764 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3106 5 %RANDOM
Rwork0.179 59001 --
obs0.181 62107 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 46.28 Å2 / Biso mean: 13.778 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2--0.67 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9055 0 16 495 9566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0229271
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.97312604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06451182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50124.504373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.223151471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0021542
X-RAY DIFFRACTIONr_chiral_restr0.1890.21489
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216924
X-RAY DIFFRACTIONr_mcbond_it0.7721.55930
X-RAY DIFFRACTIONr_mcangle_it1.37529547
X-RAY DIFFRACTIONr_scbond_it2.5333341
X-RAY DIFFRACTIONr_scangle_it3.9064.53057
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1D1188TIGHT POSITIONAL0.070.05
2A1188TIGHT POSITIONAL0.070.05
3B1188TIGHT POSITIONAL0.070.05
4C1188TIGHT POSITIONAL0.080.05
1D1061LOOSE POSITIONAL0.185
2A1061LOOSE POSITIONAL0.145
3B1061LOOSE POSITIONAL0.155
4C1061LOOSE POSITIONAL0.165
1D1188TIGHT THERMAL0.260.5
2A1188TIGHT THERMAL0.330.5
3B1188TIGHT THERMAL0.360.5
4C1188TIGHT THERMAL0.260.5
1D1061LOOSE THERMAL0.3110
2A1061LOOSE THERMAL0.3110
3B1061LOOSE THERMAL0.3510
4C1061LOOSE THERMAL0.310
LS refinement shellResolution: 2.196→2.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 218 -
Rwork0.181 4133 -
all-4351 -
obs--100 %

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