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- PDB-7et8: Crystal structure of thermostable AbHpaI, a class II metal depend... -

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Basic information

Entry
Database: PDB / ID: 7et8
TitleCrystal structure of thermostable AbHpaI, a class II metal dependent pyruvate aldolase, HpaI from Acinetobacter baumannii
Components4-hydroxy-2-oxoheptanedioate aldolase
KeywordsLYASE / TIM barrel / aldehyde lyase
Function / homology
Function and homology information


4-hydroxy-2-oxoheptanedioate aldolase / 2,4-dihydroxyhept-2-ene-1,7-dioate aldolase activity / phenylacetate catabolic process / metal ion binding
Similarity search - Function
2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase family / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
4-hydroxy-2-oxoheptanedioate aldolase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
Model detailsCrystal structure of thermostable AbHpaI, a class II metal dependent pyruvate aldolase, HpaI from ...Crystal structure of thermostable AbHpaI, a class II metal dependent pyruvate aldolase, HpaI from Acinetobacter baumannii
AuthorsWatthaisong, P. / Binlaeh, A. / Jaruwat, A. / Chaiyen, P. / Chitnumsub, P. / Maenpuen, S.
Funding support Thailand, 2items
OrganizationGrant numberCountry
National Center for Genetic Engineering and Biotechnology (Thailand)P16-52034 Thailand
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Catalytic and structural insights into a stereospecific and thermostable Class II aldolase HpaI from Acinetobacter baumannii.
Authors: Watthaisong, P. / Binlaeh, A. / Jaruwat, A. / Lawan, N. / Tantipisit, J. / Jaroensuk, J. / Chuaboon, L. / Phonbuppha, J. / Tinikul, R. / Chaiyen, P. / Chitnumsub, P. / Maenpuen, S.
History
DepositionMay 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxy-2-oxoheptanedioate aldolase
B: 4-hydroxy-2-oxoheptanedioate aldolase
C: 4-hydroxy-2-oxoheptanedioate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3084
Polymers86,2683
Non-polymers401
Water11,007611
1
A: 4-hydroxy-2-oxoheptanedioate aldolase
B: 4-hydroxy-2-oxoheptanedioate aldolase
C: 4-hydroxy-2-oxoheptanedioate aldolase
hetero molecules

A: 4-hydroxy-2-oxoheptanedioate aldolase
B: 4-hydroxy-2-oxoheptanedioate aldolase
C: 4-hydroxy-2-oxoheptanedioate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,6168
Polymers172,5356
Non-polymers802
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area25250 Å2
ΔGint-182 kcal/mol
Surface area48950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.620, 90.163, 86.484
Angle α, β, γ (deg.)90.000, 122.330, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

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Components

#1: Protein 4-hydroxy-2-oxoheptanedioate aldolase


Mass: 28755.910 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: hpaI, FD887_17235 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A5R9HKL3, 4-hydroxy-2-oxoheptanedioate aldolase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 288 K / Method: microbatch / pH: 4.6 / Details: Ca chloride, MPD, Na acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.54 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Jul 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→10 Å / Num. obs: 74317 / % possible obs: 98.5 % / Redundancy: 5.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.041 / Rrim(I) all: 0.098 / Net I/σ(I): 13.6 / Num. measured all: 396136 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.943.20.3091438745410.8450.1960.3694.497.7
9.31-1012.20.03216591360.9990.0090.03454.320.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.5.21data scaling
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V5J

2v5j


Resolution: 1.9→10 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.262 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 3097 4.9 %RANDOM
Rwork0.1691 ---
obs0.1709 59533 82.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.73 Å2 / Biso mean: 15.128 Å2 / Biso min: 3.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20.34 Å2
2---0.09 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5781 0 1 611 6393
Biso mean--12.99 23.74 -
Num. residues----759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135898
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175676
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.6137992
X-RAY DIFFRACTIONr_angle_other_deg1.4691.57413179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7355762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07424.444270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.854151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0481524
X-RAY DIFFRACTIONr_chiral_restr0.0860.2780
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021092
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 134 -
Rwork0.302 3392 -
all-3526 -
obs--62.99 %

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