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- PDB-4b5s: Crystal structures of divalent metal dependent pyruvate aldolase,... -

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Basic information

Entry
Database: PDB / ID: 4b5s
TitleCrystal structures of divalent metal dependent pyruvate aldolase, HpaI, in complex with pyruvate
Components4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
KeywordsLYASE
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
D-Glyceraldehyde / : / PHOSPHATE ION / PYRUVIC ACID / 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: 1.68 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 1.2Oct 31, 2012Group: Database references
Revision 1.3Feb 6, 2013Group: Atomic model
Revision 1.4Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 8, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_validate_chiral
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_PDB_caveat.text / _entity.pdbx_description / _entity.src_method / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_validate_chiral.label_alt_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
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)54,92414
Polymers54,0202
Non-polymers90512
Water19,6541091
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)164,77342
Polymers162,0596
Non-polymers2,71436
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area29890 Å2
ΔGint-316.1 kcal/mol
Surface area46090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.740, 151.740, 151.740
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-2074-

HOH

21A-2107-

HOH

31A-2108-

HOH

41A-2151-

HOH

51B-2078-

HOH

61B-2152-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#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: 27009.793 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI ATCC 8739 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B1IS70, 2-dehydro-3-deoxyglucarate aldolase
#2: Sugar ChemComp-3GR / D-Glyceraldehyde / GLYCERALDEHYDE / (2R)-2,3-DIHYDROXYPROPANAL / Glyceraldehyde


Type: D-saccharide / Mass: 90.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H6O3

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Non-polymers , 6 types, 1102 molecules

#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1091 / 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: 3.85 Å3/Da / Density % sol: 67.76 % / Description: WE REPORTED RPIM INSTEAD OF RMERGE
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 / Beamline: X25 / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.68→45.7 Å / Num. obs: 131767 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 21.4 % / Biso Wilson estimate: 25.54 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 19.2
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 19.15 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 100

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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: 1.68→40.554 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 18.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1789 9871 7.5 %
Rwork0.1515 --
obs0.1536 131756 99.95 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 4 Å2 / ksol: 4 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Refinement stepCycle: LAST / Resolution: 1.68→40.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 48 1091 4939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183953
X-RAY DIFFRACTIONf_angle_d1.6475387
X-RAY DIFFRACTIONf_dihedral_angle_d14.1951453
X-RAY DIFFRACTIONf_chiral_restr0.103605
X-RAY DIFFRACTIONf_plane_restr0.008712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.69910.3053250.27694053X-RAY DIFFRACTION100
1.6991-1.71910.29563270.26944027X-RAY DIFFRACTION100
1.7191-1.740.26213290.2514037X-RAY DIFFRACTION100
1.74-1.76210.26073260.24094048X-RAY DIFFRACTION100
1.7621-1.78530.2643320.23524057X-RAY DIFFRACTION100
1.7853-1.80970.26413240.22853969X-RAY DIFFRACTION100
1.8097-1.83560.23453310.22194074X-RAY DIFFRACTION100
1.8356-1.8630.24143200.21234002X-RAY DIFFRACTION100
1.863-1.89210.22023300.21144070X-RAY DIFFRACTION100
1.8921-1.92310.24113340.20544032X-RAY DIFFRACTION100
1.9231-1.95630.21263280.19684043X-RAY DIFFRACTION100
1.9563-1.99180.22423280.1994035X-RAY DIFFRACTION100
1.9918-2.03010.19773270.1814029X-RAY DIFFRACTION100
2.0301-2.07160.20943320.17774059X-RAY DIFFRACTION100
2.0716-2.11660.18573240.17114037X-RAY DIFFRACTION100
2.1166-2.16580.19243300.17264073X-RAY DIFFRACTION100
2.1658-2.220.18613290.16484044X-RAY DIFFRACTION100
2.22-2.280.19273310.15774046X-RAY DIFFRACTION100
2.28-2.34710.1823260.15154053X-RAY DIFFRACTION100
2.3471-2.42290.17243280.15484078X-RAY DIFFRACTION100
2.4229-2.50940.18513280.14554030X-RAY DIFFRACTION100
2.5094-2.60990.1693360.14034074X-RAY DIFFRACTION100
2.6099-2.72870.16383300.14234065X-RAY DIFFRACTION100
2.7287-2.87250.1843250.13774069X-RAY DIFFRACTION100
2.8725-3.05240.16053380.13844100X-RAY DIFFRACTION100
3.0524-3.2880.17793280.1364093X-RAY DIFFRACTION100
3.288-3.61870.17183260.1244100X-RAY DIFFRACTION100
3.6187-4.14190.13123310.11254114X-RAY DIFFRACTION100
4.1419-5.21660.14433290.11174153X-RAY DIFFRACTION100
5.2166-40.5660.17693390.16954221X-RAY DIFFRACTION99

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