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- PDB-4b5w: Crystal structures of divalent metal dependent pyruvate aldolase ... -

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Basic information

Entry
Database: PDB / ID: 4b5w
TitleCrystal structures of divalent metal dependent pyruvate aldolase R70A mutant, 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
: / 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: 1.792 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 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 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. THE SHEETS PRESENTED AS "CA" 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 "DA" 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 "EA" 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 "FA" 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
C: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
D: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
E: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
F: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,27923
Polymers164,1976
Non-polymers1,08217
Water33,4721858
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26160 Å2
ΔGint-212.9 kcal/mol
Surface area47750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.348, 119.144, 140.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 27366.146 Da / Num. of mol.: 6 / Fragment: RESIDUES 1-256 / Mutation: YES
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: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H4O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1858 / 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: 2.07 Å3/Da / Density % sol: 40.7 % / Description: RPIM REPORTED INSTEAD OF RMERGE
Crystal growDetails: 22% PEG 2000 MME, 10MM NICL2, 25MM HEPES PH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.79→38.5 Å / Num. obs: 127694 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Biso Wilson estimate: 17.91 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.5
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.8 / % possible all: 93.8

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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: 1.792→38.493 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 17.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1838 12761 10 %
Rwork0.1442 --
obs0.1482 127605 99.31 %
Displacement parametersBiso mean: 21.2 Å2
Refinement stepCycle: LAST / Resolution: 1.792→38.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11473 0 47 1858 13378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111719
X-RAY DIFFRACTIONf_angle_d1.25215972
X-RAY DIFFRACTIONf_dihedral_angle_d15.4024300
X-RAY DIFFRACTIONf_chiral_restr0.0731825
X-RAY DIFFRACTIONf_plane_restr0.0072134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7923-1.81260.23064030.1773628X-RAY DIFFRACTION95
1.8126-1.8340.23554260.16733830X-RAY DIFFRACTION100
1.834-1.85630.23074160.16663745X-RAY DIFFRACTION99
1.8563-1.87980.21454210.15943791X-RAY DIFFRACTION99
1.8798-1.90460.21134180.1593766X-RAY DIFFRACTION99
1.9046-1.93060.20864190.14423766X-RAY DIFFRACTION99
1.9306-1.95820.20854230.14623812X-RAY DIFFRACTION99
1.9582-1.98750.19894180.14593758X-RAY DIFFRACTION99
1.9875-2.01850.20614200.14733783X-RAY DIFFRACTION99
2.0185-2.05160.19734190.13793764X-RAY DIFFRACTION99
2.0516-2.0870.18834250.14053828X-RAY DIFFRACTION99
2.087-2.12490.18784220.13833792X-RAY DIFFRACTION100
2.1249-2.16580.20354240.1433820X-RAY DIFFRACTION99
2.1658-2.210.18214210.13393797X-RAY DIFFRACTION100
2.21-2.2580.18054250.13233823X-RAY DIFFRACTION100
2.258-2.31060.19014260.1363832X-RAY DIFFRACTION100
2.3106-2.36830.19564250.13893832X-RAY DIFFRACTION100
2.3683-2.43240.18744280.14193838X-RAY DIFFRACTION100
2.4324-2.50390.19374240.14313822X-RAY DIFFRACTION100
2.5039-2.58470.1954300.13643876X-RAY DIFFRACTION100
2.5847-2.67710.19174270.13983831X-RAY DIFFRACTION100
2.6771-2.78420.18564250.14343836X-RAY DIFFRACTION100
2.7842-2.91090.17744330.14053895X-RAY DIFFRACTION100
2.9109-3.06430.17134290.14843862X-RAY DIFFRACTION100
3.0643-3.25620.19334300.14683873X-RAY DIFFRACTION100
3.2562-3.50750.184320.14283883X-RAY DIFFRACTION100
3.5075-3.86020.16254330.13133890X-RAY DIFFRACTION100
3.8602-4.4180.15354300.12763875X-RAY DIFFRACTION99
4.418-5.56360.14554360.13833925X-RAY DIFFRACTION99
5.5636-38.50160.1954530.18444071X-RAY DIFFRACTION98

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