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- PDB-8juo: Crystal structure of aspartate semialdehyde dehydrogenase from Po... -

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Basic information

Entry
Database: PDB / ID: 8juo
TitleCrystal structure of aspartate semialdehyde dehydrogenase from Porphyromonas gingivalis
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Aspartate semialdehyde dehydrogenase
Function / homology:
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsHwang, J. / Do, H. / Lee, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)PM23030 Korea, Republic Of
CitationJournal: Crystals / Year: 2023
Title: Crystal Structure of Aspartate Semialdehyde Dehydrogenase from Porphyromonas gingivalis.
Authors: Hwang, J. / Do, H. / Shim, Y.S. / Lee, J.H.
History
DepositionJun 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate-semialdehyde dehydrogenase
B: Aspartate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)74,5992
Polymers74,5992
Non-polymers00
Water6,233346
1
A: Aspartate-semialdehyde dehydrogenase

A: Aspartate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)74,5992
Polymers74,5992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1/2,z1
Buried area5450 Å2
ΔGint-38 kcal/mol
Surface area24140 Å2
MethodPISA
2
B: Aspartate-semialdehyde dehydrogenase

B: Aspartate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)74,5992
Polymers74,5992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y+1/2,z1
Buried area5560 Å2
ΔGint-37 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.860, 108.860, 162.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2

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Components

#1: Protein Aspartate-semialdehyde dehydrogenase / ASA dehydrogenase / ASADH / Aspartate-beta-semialdehyde dehydrogenase


Mass: 37299.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: At the location of two residues at the C-terminal, the electron density map was very weak since it might be a reason for terminal flexibility.
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: asd, PGIN_13-1_01585 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1R4DY25, aspartate-semialdehyde dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M calcium acetate hydrate , 0.1 M MES: NaOH (pH 6) , 10 % (w/v) Isopropanol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.73→29.75 Å / Num. obs: 69004 / % possible obs: 99.5 % / Redundancy: 13.3 % / Biso Wilson estimate: 25.02 Å2 / CC1/2: 1 / Net I/σ(I): 19.59
Reflection shellResolution: 1.73→1.79 Å / Rmerge(I) obs: 1.269 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 6845

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→29.75 Å / SU ML: 0.1867 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 30.5138 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2378 3363 4.88 %
Rwork0.2165 65596 -
obs0.2176 68959 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.26 Å2
Refinement stepCycle: LAST / Resolution: 1.73→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 0 346 5542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00775298
X-RAY DIFFRACTIONf_angle_d0.9467180
X-RAY DIFFRACTIONf_chiral_restr0.0625808
X-RAY DIFFRACTIONf_plane_restr0.0064944
X-RAY DIFFRACTIONf_dihedral_angle_d27.80961972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.750.33281390.33282716X-RAY DIFFRACTION99.96
1.75-1.780.32031240.31252726X-RAY DIFFRACTION99.89
1.78-1.810.3061360.30372715X-RAY DIFFRACTION99.93
1.81-1.840.31111470.28362713X-RAY DIFFRACTION99.97
1.84-1.870.30921500.28562692X-RAY DIFFRACTION99.89
1.87-1.90.3261250.29092687X-RAY DIFFRACTION98.25
1.9-1.940.34561380.31652614X-RAY DIFFRACTION96.63
1.94-1.980.31361300.27092736X-RAY DIFFRACTION99.55
1.98-2.020.2641590.25452694X-RAY DIFFRACTION100
2.02-2.070.32451250.26062706X-RAY DIFFRACTION99.16
2.07-2.120.24741570.24742692X-RAY DIFFRACTION99.03
2.12-2.180.25711530.22982716X-RAY DIFFRACTION99.97
2.18-2.240.27271440.24152691X-RAY DIFFRACTION99.44
2.24-2.320.22741240.22742746X-RAY DIFFRACTION99.14
2.32-2.40.24641370.2262736X-RAY DIFFRACTION99.9
2.4-2.490.23591560.23552728X-RAY DIFFRACTION100
2.49-2.610.29741430.23472731X-RAY DIFFRACTION99.97
2.61-2.750.27481350.2442760X-RAY DIFFRACTION99.79
2.75-2.920.26821420.23712738X-RAY DIFFRACTION99.9
2.92-3.140.2461420.22522759X-RAY DIFFRACTION100
3.14-3.460.23791340.21512777X-RAY DIFFRACTION99.73
3.46-3.960.21471510.18142768X-RAY DIFFRACTION99.83
3.96-4.980.15161360.15162837X-RAY DIFFRACTION100
4.98-100.1881360.16922918X-RAY DIFFRACTION99.45

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