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- PDB-4onv: Crystal structure of YagE, a KDG aldolase protein in complex with... -

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Basic information

Entry
Database: PDB / ID: 4onv
TitleCrystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate
ComponentsProbable 2-keto-3-deoxy-galactonate aldolase YagE
KeywordsLYASE / tim barrel / NAL superfamily / Aldolase class I
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
2-KETO-3-DEOXYGLUCONATE / Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.57 Å
AuthorsManoj Kumar, P. / Bhaskar, V. / Manicka, S. / Krishnaswamy, S.
Citation
Journal: To be Published
Title: Crystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate
Authors: Manoj Kumar, P. / Bhaskar, V. / Manicka, S. / Krishnaswamy, S.
#1: Journal: Proteins / Year: 2008
Title: Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12.
Authors: Manicka, S. / Peleg, Y. / Unger, T. / Albeck, S. / Dym, O. / Greenblatt, H.M. / Bourenkov, G. / Lamzin, V. / Krishnaswamy, S. / Sussman, J.L.
#2: Journal: 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
DepositionJan 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_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_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_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: Probable 2-keto-3-deoxy-galactonate aldolase YagE
B: Probable 2-keto-3-deoxy-galactonate aldolase YagE
C: Probable 2-keto-3-deoxy-galactonate aldolase YagE
D: Probable 2-keto-3-deoxy-galactonate aldolase YagE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,89336
Polymers148,0534
Non-polymers2,84132
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17340 Å2
ΔGint-7 kcal/mol
Surface area38230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.170, 155.410, 55.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 12 - 309 / Label seq-ID: 30 - 327

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Probable 2-keto-3-deoxy-galactonate aldolase YagE / Probable KDGal aldolase YagE


Mass: 37013.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0268, JW0261, yagE / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P75682, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-KDG / 2-KETO-3-DEOXYGLUCONATE


Mass: 178.140 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 6.5
Details: 15%PEG 3350, 100mM Hepes pH 6.5, 200mM MgCl2, Microbatch under oil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.974 Å
DetectorDetector: CCD / Date: May 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 1.99→19.79 Å / Num. obs: 83685 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.405 / Net I/σ(I): 4.81
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.99-2.040.0350.44191.2
2.04-2.10.0350.69199.3
2.1-2.160.0350.9199.4
2.16-2.220.0351.11199.4
2.22-2.30.0351.28199.5
2.3-2.380.0351.58199.6
2.38-2.470.0351.93199.5
2.47-2.570.0352.33199.5
2.57-2.680.0352.73199.6
2.68-2.810.0353.02199.5
2.81-2.960.0353.74199.5
2.96-3.140.0354.92199.4
3.14-3.360.0356.87199.3
3.36-3.630.0359.5199.1
3.63-3.980.03511.75199
3.98-4.450.03514.67199
4.45-5.130.03515.94198.8
5.13-6.290.03512.9199.1
6.29-8.890.03519.96198.4
8.890.03530.87187.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→19.79 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.879 / SU B: 13.446 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2845 1970 5 %RANDOM
Rwork0.24658 ---
obs0.24848 37422 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.637 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å2-0 Å20 Å2
2--4.22 Å2-0 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.57→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9037 0 182 200 9419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0199395
X-RAY DIFFRACTIONr_bond_other_d0.0050.029177
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9812737
X-RAY DIFFRACTIONr_angle_other_deg1.186321094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00451190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23624.453375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.102151487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3251544
X-RAY DIFFRACTIONr_chiral_restr0.0830.21504
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110524
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022032
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2292.214769
X-RAY DIFFRACTIONr_mcbond_other1.2282.214768
X-RAY DIFFRACTIONr_mcangle_it1.9653.3115956
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3162.3614626
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A183090.1
12B183090.1
21A182400.1
22C182400.1
31A183440.1
32D183440.1
41B182890.1
42C182890.1
51B187280.09
52D187280.09
61C185420.1
62D185420.1
LS refinement shellResolution: 2.57→2.636 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 142 -
Rwork0.317 2699 -
obs--99.54 %

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