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- PDB-6ofu: X-ray crystal structure of the YdjI aldolase from Escherichia coli K12 -

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Basic information

Entry
Database: PDB / ID: 6ofu
TitleX-ray crystal structure of the YdjI aldolase from Escherichia coli K12
ComponentsYdjI aldolase
KeywordsLYASE / aldolase
Function / homology
Function and homology information


tagatose-bisphosphate aldolase activity / aldehyde-lyase activity / protein homotetramerization / carbohydrate metabolic process / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
: / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein YdjI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDopkins, B.J. / Thoden, J.B. / Huddleston, J.P. / Narindoshvili, T. / Fose, B. / Rachel, F.M. / Holden, H.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122825 United States
Robert A. Welch FoundationA-840 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity inEscherichia coliK12.
Authors: Huddleston, J.P. / Thoden, J.B. / Dopkins, B.J. / Narindoshvili, T. / Fose, B.J. / Holden, H.M. / Raushel, F.M.
History
DepositionApr 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_ptnr1_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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.5Nov 15, 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

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Assembly

Deposited unit
A: YdjI aldolase
B: YdjI aldolase
C: YdjI aldolase
D: YdjI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,26211
Polymers127,8644
Non-polymers3987
Water17,997999
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-252 kcal/mol
Surface area38260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.763, 85.663, 84.268
Angle α, β, γ (deg.)90.00, 109.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
YdjI aldolase


Mass: 31965.918 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ydjI, b1773, JW1762 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P77704
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10-12% PEG5000 100 mM MES 5 mM DHAP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 104686 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 33.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 7205 / Rsym value: 0.213 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gvf

1gvf


Resolution: 1.75→34.74 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.981 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18156 5200 5 %RANDOM
Rwork0.14145 ---
obs0.14342 99486 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.881 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.32 Å2
2--0.33 Å20 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.75→34.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8115 0 7 999 9121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0158316
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177442
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.72111267
X-RAY DIFFRACTIONr_angle_other_deg0.4911.70817367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02451038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79419.654289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.033151149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2991541
X-RAY DIFFRACTIONr_chiral_restr0.0720.21106
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029405
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021567
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_it2.1012.1774161
X-RAY DIFFRACTIONr_mcbond_other2.1012.1774162
X-RAY DIFFRACTIONr_mcangle_it2.9613.2435184
X-RAY DIFFRACTIONr_mcangle_other2.9643.2445185
X-RAY DIFFRACTIONr_scbond_it3.3442.5474155
X-RAY DIFFRACTIONr_scbond_other3.3432.5454154
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0423.6776080
X-RAY DIFFRACTIONr_long_range_B_refined6.04428.5929464
X-RAY DIFFRACTIONr_long_range_B_other5.87427.899173
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.752→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 349 -
Rwork0.192 6890 -
obs--90.5 %

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