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- PDB-4oe7: Crystal structure of YagE, a KDG aldolase protein, in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4oe7
TitleCrystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal
ComponentsProbable 2-keto-3-deoxy-galactonate aldolase YagE
KeywordsLYASE / tim barrel / aldolase type I / sugar binding / metal coordination / schiff base
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
(4S)-4-hydroxy-2,5-dioxopentanoic acid / (4R)-4-hydroxy-2,5-dioxopentanoic acid / ethanedial / PYRUVIC ACID / Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsManoj Kumar, P. / Baskar, V. / Manicka, S. / Krishnaswamy, S.
Citation
Journal: To be Published
Title: Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal
Authors: Manoj Kumar, P. / Baskar, 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 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_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)151,10547
Polymers148,0534
Non-polymers3,05243
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18080 Å2
ΔGint1 kcal/mol
Surface area37120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.240, 155.140, 55.580
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
21C
12D
22B

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 1 / Auth seq-ID: 12 - 309 / Label seq-ID: 30 - 327

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
12DD
22BB

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ABCD

#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: K12 / 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

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Non-polymers , 8 types, 248 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GXT / ethanedial


Mass: 58.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H2O2
#6: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#7: Chemical ChemComp-GXP / (4S)-4-hydroxy-2,5-dioxopentanoic acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#8: Chemical ChemComp-GXS / (4R)-4-hydroxy-2,5-dioxopentanoic acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 6.5
Details: 100mM HEPES pH 6.5, 200mM Magnesium chloride, 15% PEG 3350, MICROBATCH UNDER OIL, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorDetector: CCD / Date: May 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.99→8.89 Å / Num. obs: 83414 / % possible obs: 98.2 % / Redundancy: 4.1 % / Net I/σ(I): 14.43
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 3.42 % / Mean I/σ(I) obs: 2.76 / % possible all: 87

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V8Z

2v8z


Resolution: 1.99→49.06 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.971 / SU ML: 0.111 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23308 4171 5 %RANDOM
Rwork0.19804 ---
obs0.1998 79242 98.27 %-
all-83414 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.011 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å2-0 Å20 Å2
2--1.1 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.99→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9037 0 192 205 9434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0199393
X-RAY DIFFRACTIONr_bond_other_d0.010.029179
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.97812700
X-RAY DIFFRACTIONr_angle_other_deg1.356321087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22951188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37824.439374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.478151483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0451544
X-RAY DIFFRACTIONr_chiral_restr0.1270.21491
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110525
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022034
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_it1.4361.7654769
X-RAY DIFFRACTIONr_mcbond_other1.4351.7654770
X-RAY DIFFRACTIONr_mcangle_it1.9462.6355948
X-RAY DIFFRACTIONr_mcangle_other1.9432.6375949
X-RAY DIFFRACTIONr_scbond_it2.1612.0214624
X-RAY DIFFRACTIONr_scbond_other2.192.0234623
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1912.936754
X-RAY DIFFRACTIONr_long_range_B_refined4.10514.61610667
X-RAY DIFFRACTIONr_long_range_B_other4.10614.61510666
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: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A44950.99
22D45031.13
LS refinement shellResolution: 1.988→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 267 -
Rwork0.273 5078 -
obs--87.09 %

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