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- PDB-2v5j: Apo Class II aldolase HpcH -

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Basic information

Entry
Database: PDB / ID: 2v5j
TitleApo Class II aldolase HpcH
Components2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE
KeywordsLYASE / CLASS II ALDOLASE / HOMOPROTOCATECHUATE / AROMATIC DEGRADATION / AROMATIC HYDROCARBONS CATABOLISM
Function / homology
Function and homology information


4-hydroxy-2-ketopimelate aldolase activity / 4-hydroxy-2-oxoheptanedioate aldolase / : / 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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 5, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "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)62,9219
Polymers62,2712
Non-polymers6507
Water9,206511
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)188,76327
Polymers186,8126
Non-polymers1,95121
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area29870 Å2
ΔGint-210.5 kcal/mol
Surface area62050 Å2
MethodPQS
Unit cell
Length a, b, c (Å)128.920, 128.920, 175.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2061-

HOH

21A-2063-

HOH

31B-2065-

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-PO4 / PHOSPHATE ION


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.3 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 5
Details: 0.4 M AMMONIUM DIHYDROGEN PHOSPHATE, 30% (V/V) GLYCEROL, pH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: May 2, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→40.8 Å / Num. obs: 73671 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 33.6
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DXE

1dxe


Resolution: 1.6→40.79 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.93 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2982 4 %RANDOM
Rwork0.173 ---
obs0.174 70689 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4007 0 40 511 4558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224117
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9765604
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2175527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21924.807181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74315652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4191528
X-RAY DIFFRACTIONr_chiral_restr0.0950.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023148
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.22058
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22884
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2381
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.2121
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9351.52684
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48524213
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.49531598
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9914.51391
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 221
Rwork0.242 5165
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)
10.79960.93881.07693.52272.36011.9465-0.00030.1717-0.049-0.07080.2093-0.3130.0820.391-0.2091-0.01930.0134-0.00520.1175-0.01410.056629.2250.09259.529
20.30390.08290.04080.61420.2571.17090.0067-0.04660.01680.0890.0025-0.0477-0.02340.0841-0.0092-0.0775-0.0131-0.0132-0.05030.0023-0.042317.058.96667.615
30.2209-1.21480.77288.533-7.21777.46-0.02290.04690.0760.07130.07790.0346-0.5246-0.0347-0.0550.1017-0.04-0.0413-0.06590.02220.03537.34630.73844.253
41.53041.826-1.41653.7204-3.15072.69480.07940.09960.41690.1980.2420.3386-0.3093-0.3153-0.32140.06260.05930.00140.00770.02980.0723-14.39925.4136.728
50.47710.1368-0.09820.6439-0.51441.506-0.03140.11670.052-0.15160.00550.01890.00430.01110.02580.00050.0021-0.0131-0.05810.0199-0.0351-0.6219.38828.634
66.38192.38747.1431.18562.51989.3903-0.08440.30830.09940.1221-0.0134-0.1276-0.41450.68580.09780.0247-0.0858-0.02690.02310.04460.016419.21820.83248.479
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-8 - 14
2X-RAY DIFFRACTION2A15 - 233
3X-RAY DIFFRACTION3A234 - 259
4X-RAY DIFFRACTION4B-8 - 14
5X-RAY DIFFRACTION5B15 - 233
6X-RAY DIFFRACTION6B234 - 252

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