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- PDB-7et9: Crystal structure of AbHpaI-Zn-pyruvate complex, Class II aldolas... -

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Basic information

Entry
Database: PDB / ID: 7et9
TitleCrystal structure of AbHpaI-Zn-pyruvate complex, Class II 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 / 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 / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
PYRUVIC ACID / 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 AbHpaI-Zn-pyruvate complex, a class II 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: 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)86,76810
Polymers86,2683
Non-polymers5007
Water8,593477
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)173,53620
Polymers172,5356
Non-polymers1,00114
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area27790 Å2
ΔGint-383 kcal/mol
Surface area48970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.919, 89.669, 86.491
Angle α, β, γ (deg.)90.000, 122.740, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 28755.910 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-266
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-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 288 K / Method: microbatch / pH: 4.6 / Details: CaCl2, 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 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.74→21.09 Å / Num. obs: 85669 / % possible obs: 88.4 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.031 / Rrim(I) all: 0.083 / Net I/σ(I): 15.9 / Num. measured all: 550140 / Scaling rejects: 97
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
1.74-1.771.40.575207214360.4940.4710.748228.2
9.22-21.096.10.03633295430.9990.0150.03940.978.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ET8

7et8


Resolution: 1.9→20.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.412 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1848 3680 5.2 %RANDOM
Rwork0.1553 ---
obs0.1569 67173 94.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.58 Å2 / Biso mean: 13.343 Å2 / Biso min: 4.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20.11 Å2
2--0.04 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.9→20.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5805 0 22 477 6304
Biso mean--15.1 19.81 -
Num. residues----762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135907
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165838
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.6278004
X-RAY DIFFRACTIONr_angle_other_deg1.4491.5813413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3315759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63624.348276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.359151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8881524
X-RAY DIFFRACTIONr_chiral_restr0.0810.2780
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021257
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 193 -
Rwork0.235 3172 -
all-3365 -
obs--60.57 %

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