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- PDB-4b5x: Crystal structures of divalent metal dependent pyruvate aldolase ... -

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Basic information

Entry
Database: PDB / ID: 4b5x
TitleCrystal structures of divalent metal dependent pyruvate aldolase (HpaI), mutant D42A
Components4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
KeywordsLYASE / CATALYTIC MECHANISM
Function / homology
Function and homology information


4-hydroxy-2-ketopimelate aldolase activity / 4-hydroxy-2-oxoheptanedioate aldolase / 2,4-dihydroxyhept-2-ene-1,7-dioate aldolase activity / phenylacetate catabolic process / metal ion binding
Similarity search - Function
4-hydroxy-2-oxo-heptane-1,7-dioate aldolase, Enterobacteriales / 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase family / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI ATCC 8739 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCoincon, M. / Wang, W. / Seah, S.Y.K. / Sygusch, J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of Reaction Intermediates in Pyruvate Class II Aldolase: Substrate Cleavage, Enolate Stabilization and Substrate Specificity
Authors: Coincon, M. / Wang, W. / Sygusch, J. / Seah, S.Y.K.
History
DepositionAug 7, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Atomic model / Database references
Revision 1.2Sep 26, 2012Group: Atomic model
Revision 1.3Oct 31, 2012Group: Database references
Revision 1.4Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
B: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,05012
Polymers56,1062
Non-polymers94410
Water16,141896
1
A: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
B: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
hetero molecules

A: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
B: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
hetero molecules

A: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
B: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,15036
Polymers168,3186
Non-polymers2,83230
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area31700 Å2
ΔGint-344.3 kcal/mol
Surface area48100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.170, 151.170, 151.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-2123-

HOH

21A-2126-

HOH

31B-2113-

HOH

41B-2120-

HOH

51B-2390-

HOH

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Components

#1: Protein 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE / HPAI / 2 / 4-DIHYDROXYHEPT-2-ENE-1 / 7-DIOIC ACID ALDOLASE / HHED ALDOLASE / 4-HYDROXY-2- ...HPAI / 2 / 4-DIHYDROXYHEPT-2-ENE-1 / 7-DIOIC ACID ALDOLASE / HHED ALDOLASE / 4-HYDROXY-2-KETOHEPTANE-1 / 7-DIOATE ALDOLASE / HKHD ALDOLASE


Mass: 28053.037 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI ATCC 8739 (bacteria) / Plasmid: PT7-7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B1IS70, 2-dehydro-3-deoxyglucarate aldolase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 896 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 68.75 % / Description: NONE
Crystal growDetails: 0.5 M AMMONIUM DIHYDROGEN PHOSPHATE, 30% GLYCEROL, 2 MM COCL2 PH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Type: NSLS / Wavelength: 1.0809
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.8→30.86 Å / Num. obs: 103465 / % possible obs: 97.5 % / Observed criterion σ(I): 1 / Redundancy: 17.8 % / Biso Wilson estimate: 26.64 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 16.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.8 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V5J

2v5j


Resolution: 1.8→30.234 Å / SU ML: 0.19 / σ(F): 1.33 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1928 10328 10 %
Rwork0.1649 --
obs0.1677 103400 97.42 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 4 Å2 / ksol: 4 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 52 896 4756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173922
X-RAY DIFFRACTIONf_angle_d1.4755345
X-RAY DIFFRACTIONf_dihedral_angle_d14.5991435
X-RAY DIFFRACTIONf_chiral_restr0.111604
X-RAY DIFFRACTIONf_plane_restr0.007703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.34422940.31682582X-RAY DIFFRACTION83
1.8205-1.84190.30483070.30482707X-RAY DIFFRACTION85
1.8419-1.86440.30833100.29522706X-RAY DIFFRACTION87
1.8644-1.88790.28193220.27992832X-RAY DIFFRACTION90
1.8879-1.91280.28273260.2642916X-RAY DIFFRACTION91
1.9128-1.9390.27712960.2392969X-RAY DIFFRACTION94
1.939-1.96670.25353320.23593063X-RAY DIFFRACTION96
1.9667-1.9960.23813380.22523106X-RAY DIFFRACTION98
1.996-2.02720.26143470.21813140X-RAY DIFFRACTION99
2.0272-2.06040.22943430.2083144X-RAY DIFFRACTION100
2.0604-2.0960.21583700.20673175X-RAY DIFFRACTION100
2.096-2.13410.22463530.19253170X-RAY DIFFRACTION100
2.1341-2.17510.23473470.18473103X-RAY DIFFRACTION100
2.1751-2.21950.20513540.17853213X-RAY DIFFRACTION100
2.2195-2.26770.20113540.17213173X-RAY DIFFRACTION100
2.2677-2.32050.20443490.1813161X-RAY DIFFRACTION100
2.3205-2.37850.21083560.17653199X-RAY DIFFRACTION100
2.3785-2.44280.20923430.17213153X-RAY DIFFRACTION100
2.4428-2.51460.20353530.1723176X-RAY DIFFRACTION100
2.5146-2.59570.19883510.16033205X-RAY DIFFRACTION100
2.5957-2.68840.18643480.15363163X-RAY DIFFRACTION100
2.6884-2.7960.18993610.15753192X-RAY DIFFRACTION100
2.796-2.92320.19053500.15443180X-RAY DIFFRACTION100
2.9232-3.07710.19663490.14873211X-RAY DIFFRACTION100
3.0771-3.26970.17843640.1453193X-RAY DIFFRACTION100
3.2697-3.52180.16723570.13443211X-RAY DIFFRACTION100
3.5218-3.87560.15523510.12733217X-RAY DIFFRACTION100
3.8756-4.43490.14263630.11953214X-RAY DIFFRACTION100
4.4349-5.58170.14913650.13053256X-RAY DIFFRACTION100
5.5817-30.23830.21533750.19813342X-RAY DIFFRACTION100

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