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- PDB-7etb: Crystal structure of AbHpaI-Mn-pyruvate complex, Class II aldolas... -

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Basic information

Entry
Database: PDB / ID: 7etb
TitleCrystal structure of AbHpaI-Mn-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: 1.85 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)86,73710
Polymers86,2683
Non-polymers4697
Water12,629701
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)173,47420
Polymers172,5356
Non-polymers93814
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area27670 Å2
ΔGint-186 kcal/mol
Surface area48920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.724, 90.345, 86.600
Angle α, β, γ (deg.)90.000, 122.260, 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
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#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.: 701 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
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 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 81847 / % possible obs: 99.6 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.025 / Rrim(I) all: 0.076 / Χ2: 1.025 / Net I/σ(I): 12.7 / Num. measured all: 681396
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.922.80.22279220.9090.1490.2690.48596.8
1.92-1.994.70.18681120.9610.0930.2090.5899.8
1.99-2.086.90.14782040.9840.060.1590.695100
2.08-2.198.50.12981770.9910.0470.1370.936100
2.19-2.33100.12182180.9940.040.1281.079100
2.33-2.5110.40.09682310.9960.0310.1011.068100
2.51-2.7610.40.08181580.9970.0260.0851.098100
2.76-3.1610.20.07182270.9980.0230.0751.151100
3.16-3.989.80.05682700.9980.0190.0591.172100
3.98-309.20.04883280.9990.0160.0511.16199.6

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Processing

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

7et8


Resolution: 1.85→28.45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.022 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1769 8291 10.1 %RANDOM
Rwork0.1459 ---
obs0.149 73431 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.77 Å2 / Biso mean: 16.822 Å2 / Biso min: 9.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.15 Å2
2---0.01 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.85→28.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5781 0 22 701 6504
Biso mean--13.23 25.15 -
Num. residues----759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135907
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175658
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.627971
X-RAY DIFFRACTIONr_angle_other_deg1.5031.57413131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4245756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.11224.286273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.701151041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4891524
X-RAY DIFFRACTIONr_chiral_restr0.0910.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026582
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021086
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 583 -
Rwork0.206 5251 -
all-5834 -
obs--96.22 %

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