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- PDB-7eth: Crystal structure of AbHpaI-Zn-pyruvate-propionaldehyde complex, ... -

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Basic information

Entry
Database: PDB / ID: 7eth
TitleCrystal structure of AbHpaI-Zn-pyruvate-propionaldehyde 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 family / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
PROPANAL / PYRUVIC ACID / 4-hydroxy-2-oxoheptanedioate aldolase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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)86,94213
Polymers86,2683
Non-polymers67510
Water5,044280
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)173,88526
Polymers172,5356
Non-polymers1,34920
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area28940 Å2
ΔGint-361 kcal/mol
Surface area48560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.183, 89.643, 86.312
Angle α, β, γ (deg.)90.000, 122.550, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#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

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Non-polymers , 5 types, 290 molecules

#2: Chemical ChemComp-PYR / PYRUVIC ACID


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


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


Mass: 58.079 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H6O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.78 Å3/Da / Density % sol: 55.78 %
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: May 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.19→20.85 Å / Num. obs: 48442 / % possible obs: 99.6 % / Redundancy: 8.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.054 / Rrim(I) all: 0.16 / Net I/σ(I): 11
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
2.19-2.2650.4742079241270.8740.2290.5293.898.3
9.03-20.718.60.03254466310.9990.0110.03425.787.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ET8

7et8


Resolution: 2.2→20.71 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.562 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 2379 5 %RANDOM
Rwork0.175 ---
obs0.1769 45439 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.57 Å2 / Biso mean: 12.121 Å2 / Biso min: 1.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å2-0.32 Å2
2--0.55 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.2→20.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5736 0 34 280 6050
Biso mean--20.82 13.97 -
Num. residues----753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135863
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175622
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.6217917
X-RAY DIFFRACTIONr_angle_other_deg1.4221.57813047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3275750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47924.286273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.446151029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.441524
X-RAY DIFFRACTIONr_chiral_restr0.0880.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021083
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 183 -
Rwork0.227 3350 -
all-3533 -
obs--98.96 %

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