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

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Basic information

Entry
Database: PDB / ID: 4ptn
TitleCrystal Structure of YagE, a KDG aldolase protein in complex with Magnesium cation coordinated L-glyceraldehyde
ComponentsProbable 2-keto-3-deoxy-galactonate aldolase YagE
KeywordsLYASE / tim barrel / NAL superfamily / Aldolase class I / Metal coordination / STEREOSPECIFICITY
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
L-glyceraldehyde / 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 / molecular replacement / Resolution: 1.99 Å
AuthorsManoj Kumar, P. / Baskar, V. / Manicka, S. / Krishnaswamy, S.
Citation
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.
#1: 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
DepositionMar 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 8, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_ref_seq_dif.details
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_ncs_dom_lim / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.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_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)149,46126
Polymers148,0534
Non-polymers1,40822
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13570 Å2
ΔGint-51 kcal/mol
Surface area37140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.200, 155.070, 55.400
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-597-

HOH

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

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Protein / Sugars , 2 types, 8 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
#3: Sugar
ChemComp-GXV / L-glyceraldehyde / Glyceraldehyde / (2S)-2,3-dihydroxypropanal


Type: L-saccharide / Mass: 90.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H6O3

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Non-polymers , 5 types, 543 molecules

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


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.05 Å3/Da / Density % sol: 39.95 %
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: 0.976 Å
DetectorDetector: CCD / Date: May 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.99→48.94 Å / Num. obs: 83868 / % possible obs: 99 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.14
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.99-2.040.5314.13189.4
2.04-2.090.4355.79199.7
2.09-2.160.3596.91199.7
2.16-2.220.2968.05199.7
2.22-2.290.2559.16199.7
2.29-2.380.21510.58199.9
2.38-2.470.17912.14199.7
2.47-2.570.14914.05199.9
2.57-2.680.1315.73199.9
2.68-2.810.12116.57199.8
2.81-2.960.10218.94199.7
2.96-3.140.0822.68199.9
3.14-3.360.06227.81199.8
3.36-3.630.04933.28199.8
3.63-3.970.04336.83199.7
3.97-4.440.03740.92199.7
4.44-5.130.03442.02199.9
5.13-6.280.03837.05199.9
6.28-8.890.02942.74199.9
8.890.02148.89198.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.22 Å48.94 Å
Translation8.22 Å48.94 Å

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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: 1.99→48.94 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.242 / SU ML: 0.091 / SU R Cruickshank DPI: 0.1726 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20332 4194 5 %RANDOM
Rwork0.17438 ---
obs0.17583 79674 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.539 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0 Å20 Å2
2--1.3 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.99→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9043 0 90 525 9658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199357
X-RAY DIFFRACTIONr_bond_other_d0.0090.029134
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.97512696
X-RAY DIFFRACTIONr_angle_other_deg1.348320984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1651192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92624.392378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.083151490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8641546
X-RAY DIFFRACTIONr_chiral_restr0.1140.21493
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02110564
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022050
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_it1.3471.4914768
X-RAY DIFFRACTIONr_mcbond_other1.3461.4914767
X-RAY DIFFRACTIONr_mcangle_it1.8522.2275954
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2521.7454589
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)
11A186580.09
12B186580.09
21A191210.06
22C191210.06
31A186160.09
32D186160.09
41B187260.09
42C187260.09
51B190230.07
52D190230.07
61C187410.08
62D187410.08
LS refinement shellResolution: 1.987→2.039 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 276 -
Rwork0.233 5241 -
obs--89.55 %

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