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- PDB-2v5k: Class II aldolase HpcH - magnesium - oxamate complex -

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Basic information

Entry
Database: PDB / ID: 2v5k
TitleClass II aldolase HpcH - magnesium - oxamate complex
Components2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE
KeywordsLYASE / CLASS II ALDOLASE / HOMOPROTOCATECHUATE / AROMATIC DEGRADATION / AROMATIC HYDROCARBONS CATABOLISMHOMOPROTOCATECHUATE
Function / homology
Function and homology information


4-hydroxy-2-ketopimelate aldolase activity / 4-hydroxyphenylacetate catabolic process / 4-hydroxy-2-oxoheptanedioate aldolase / phenylacetate catabolic process / metal ion binding / cytoplasm
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 / 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
OXAMIC ACID / PHOSPHATE ION / 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRea, D. / Fulop, V. / Bugg, T.D.H. / Roper, D.I.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure and Mechanism of Hpch: A Metal Ion Dependent Class II Aldolase from the Homoprotocatechuate Degradation Pathway of Escherichia Coli.
Authors: Rea, D. / Fulop, V. / Bugg, T.D.H. / Roper, D.I.
History
DepositionJul 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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_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_conn.ptnr2_symmetry / _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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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: 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE
B: 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6878
Polymers62,2712
Non-polymers4176
Water5,260292
1
A: 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE
B: 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE
hetero molecules

A: 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE
B: 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE
hetero molecules

A: 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE
B: 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,06224
Polymers186,8126
Non-polymers1,25018
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area25850 Å2
ΔGint-227.9 kcal/mol
Surface area60610 Å2
MethodPQS
Unit cell
Length a, b, c (Å)152.200, 152.200, 152.200
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-2033-

HOH

21B-2036-

HOH

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Components

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


Mass: 31135.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834
References: UniProt: Q47098, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 25 RESIDUES CONSTITUTE THE HIS-TAG AND LINKER REGION OF THE OVEREXPRESSION CONSTRUCT.

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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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 5
Details: 0.4 M AMMONIUM DIHYDROGEN PHOSPHATE, 30% (V/V) GLYCEROL, 0.01M MAGNESIUM CHLORIDE AND 0.01M SODIUM OXAMATE., pH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 9, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→50.8 Å / Num. obs: 59541 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.5
Reflection shellResolution: 2.2→2.23 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DXE

1dxe


Resolution: 2.2→50.77 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.359 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2350 3.9 %RANDOM
Rwork0.171 ---
obs0.171 57191 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.77 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3948 0 24 292 4264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224040
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9745502
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5735516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18224.778180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74215644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5941528
X-RAY DIFFRACTIONr_chiral_restr0.0890.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21766
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22750
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2253
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6921.52670
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15824134
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.14831572
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4534.51368
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
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 154 -
Rwork0.227 4199 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5836-2.4091-0.692710.99623.7681.6073-0.01360.1005-0.0637-1.38180.1361-1.2466-0.38640.2951-0.12250.1553-0.04120.21330.0725-0.05820.088170.34146.88629.114
21.06260.23740.18992.15840.44281.1188-0.01640.1369-0.2488-0.26490.0454-0.05030.0389-0.0001-0.029-0.02230.02890.0683-0.0955-0.0332-0.020559.96135.76536.867
39.3608-1.547810.66160.5703-1.01813.90840.284-0.2297-0.62650.14730.1081-0.2260.7544-0.1887-0.39220.02740.06890.0105-0.10560.0480.142271.40932.94261.909
413.0135-1.7746.22360.3054-0.70273.31020.0121-1.6478-0.970.00680.17490.03550.191-0.5625-0.1870.039-0.0218-0.01030.1530.24650.078560.34942.28983.538
51.95940.02910.37061.10570.22221.19520.0014-0.2407-0.04880.10310.0064-0.23130.01110.0565-0.0077-0.0990.0288-0.0127-0.03220.0742-0.038372.95250.95675.928
61.7893-1.8427-0.775510.154610.428311.56660.17660.1085-0.3167-0.05610.3535-0.79640.02540.5428-0.5301-0.07020.06010.0332-0.04010.01920.165976.88336.99752.264
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-8 - 0
2X-RAY DIFFRACTION1A1 - 14
3X-RAY DIFFRACTION2A15 - 233
4X-RAY DIFFRACTION3A234 - 251
5X-RAY DIFFRACTION4B-8 - 0
6X-RAY DIFFRACTION4B1 - 14
7X-RAY DIFFRACTION5B15 - 233
8X-RAY DIFFRACTION6B234 - 251

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