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- PDB-4b5u: Crystal structures of divalent metal dependent pyruvate aldolase,... -

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Basic information

Entry
Database: PDB / ID: 4b5u
TitleCrystal structures of divalent metal dependent pyruvate aldolase, HpaI, in complex with pyruvate and succinic semialdehyde
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
: / PYRUVIC ACID / 4-oxobutanoic 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: 1.913 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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)54,75112
Polymers54,0202
Non-polymers73110
Water14,556808
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)164,25236
Polymers162,0596
Non-polymers2,19330
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area30150 Å2
ΔGint-240.9 kcal/mol
Surface area45010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.130, 151.130, 151.130
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-2066-

HOH

21A-2137-

HOH

31B-2105-

HOH

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Components

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Protein , 1 types, 2 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) / Plasmid: PT7-7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B1IS70, 2-dehydro-3-deoxyglucarate aldolase

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Non-polymers , 6 types, 818 molecules

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


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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
#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-SSN / 4-oxobutanoic acid / Succinic semialdehyde / Succinic semialdehyde


Mass: 102.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 808 / Source method: isolated from a natural source / Formula: H2O

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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: 4.02 Å3/Da / Density % sol: 69.17 % / 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: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.91→41.9 Å / Num. obs: 87289 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 21.8 % / Biso Wilson estimate: 18.75 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.1
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.9 / % possible all: 81.7

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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: 1.913→41.916 Å / SU ML: 0.13 / σ(F): 2 / Phase error: 12.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1539 6546 7.5 %
Rwork0.1304 --
obs0.1322 87275 98.64 %
Solvent computationShrinkage radii: 1.4 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 4 Å2 / ksol: 4 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Refinement stepCycle: LAST / Resolution: 1.913→41.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 42 808 4650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143933
X-RAY DIFFRACTIONf_angle_d1.3875343
X-RAY DIFFRACTIONf_dihedral_angle_d16.8241461
X-RAY DIFFRACTIONf_chiral_restr0.087603
X-RAY DIFFRACTIONf_plane_restr0.006712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.913-1.93480.26831330.25341645X-RAY DIFFRACTION62
1.9348-1.95750.23432150.20282646X-RAY DIFFRACTION97
1.9575-1.98140.22822180.18762692X-RAY DIFFRACTION100
1.9814-2.00650.18932180.17012689X-RAY DIFFRACTION100
2.0065-2.03290.18852200.15732717X-RAY DIFFRACTION100
2.0329-2.06070.18092230.14612740X-RAY DIFFRACTION100
2.0607-2.09020.16452170.14052684X-RAY DIFFRACTION100
2.0902-2.12140.15732180.13192690X-RAY DIFFRACTION100
2.1214-2.15450.15122230.13812740X-RAY DIFFRACTION100
2.1545-2.18980.15242190.12812714X-RAY DIFFRACTION100
2.1898-2.22760.15412200.13372701X-RAY DIFFRACTION100
2.2276-2.26810.15252200.13332722X-RAY DIFFRACTION100
2.2681-2.31170.15522210.12612725X-RAY DIFFRACTION100
2.3117-2.35890.16362200.12392715X-RAY DIFFRACTION100
2.3589-2.41020.14042170.12222675X-RAY DIFFRACTION100
2.4102-2.46630.16112220.12492732X-RAY DIFFRACTION100
2.4663-2.52790.15592190.11862698X-RAY DIFFRACTION100
2.5279-2.59630.1512220.1252751X-RAY DIFFRACTION100
2.5963-2.67270.15832200.12042702X-RAY DIFFRACTION100
2.6727-2.75890.14422230.12252751X-RAY DIFFRACTION100
2.7589-2.85750.16462200.12562714X-RAY DIFFRACTION100
2.8575-2.97190.15822200.12432714X-RAY DIFFRACTION100
2.9719-3.10710.1472240.1222763X-RAY DIFFRACTION100
3.1071-3.27080.14622200.1182717X-RAY DIFFRACTION100
3.2708-3.47570.1372210.11442730X-RAY DIFFRACTION100
3.4757-3.74390.13512250.11182765X-RAY DIFFRACTION100
3.7439-4.12030.11932240.10782771X-RAY DIFFRACTION100
4.1203-4.71590.12912230.10682752X-RAY DIFFRACTION100
4.7159-5.93880.1422280.13362805X-RAY DIFFRACTION100
5.9388-41.9260.18462330.1792869X-RAY DIFFRACTION100

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