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

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Basic information

Entry
Database: PDB / ID: 8jus
TitleCrystal structure of aspartate semialdehyde dehydrogenase from Porphyromonas gingivalis complexed with 2',5'adenosine diphosphate
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Aspartate semialdehyde dehydrogenase
Function / homologyADENOSINE-2'-5'-DIPHOSPHATE / :
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,4544
Polymers74,5992
Non-polymers8542
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Each monomer is formed bound with 2',5'-ADP compound.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-44 kcal/mol
Surface area24180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.990, 108.220, 160.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,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: aspartate semialdehyde dehydrogenase complexed with 2',5'-adenosine diphosphate. Two C-terminal residues have weak electron density map.
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: Chemical ChemComp-A2P / ADENOSINE-2'-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium sulfate, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350

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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: May 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→28.77 Å / Num. obs: 68236 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 16.54 Å2 / CC1/2: 1 / Net I/σ(I): 29.89
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 7.46 / Num. unique obs: 6742 / CC1/2: 0.98

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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→28.77 Å / SU ML: 0.1669 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.6857 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2065 3413 5 %
Rwork0.1843 64818 -
obs0.1854 68231 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.44 Å2
Refinement stepCycle: LAST / Resolution: 1.73→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 54 419 5669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01185356
X-RAY DIFFRACTIONf_angle_d1.11547270
X-RAY DIFFRACTIONf_chiral_restr0.0663816
X-RAY DIFFRACTIONf_plane_restr0.0068946
X-RAY DIFFRACTIONf_dihedral_angle_d26.51741974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.750.23681400.21132661X-RAY DIFFRACTION100
1.75-1.780.25891430.20852699X-RAY DIFFRACTION100
1.78-1.810.23791380.19692634X-RAY DIFFRACTION100
1.81-1.840.2461420.1942685X-RAY DIFFRACTION100
1.84-1.870.24661410.18422691X-RAY DIFFRACTION100
1.87-1.90.22321400.18862648X-RAY DIFFRACTION100
1.9-1.940.22851420.19422702X-RAY DIFFRACTION100
1.94-1.980.25421400.19352667X-RAY DIFFRACTION100
1.98-2.020.22471400.18992651X-RAY DIFFRACTION100
2.02-2.070.22631420.19712713X-RAY DIFFRACTION100
2.07-2.120.21131420.19592698X-RAY DIFFRACTION100
2.12-2.180.22371400.19452649X-RAY DIFFRACTION100
2.18-2.240.21041410.1892682X-RAY DIFFRACTION100
2.24-2.320.21420.18162707X-RAY DIFFRACTION100
2.32-2.40.21581420.18572683X-RAY DIFFRACTION100
2.4-2.490.20661420.19062711X-RAY DIFFRACTION100
2.49-2.610.19341430.19322701X-RAY DIFFRACTION100
2.61-2.750.20971420.19662716X-RAY DIFFRACTION100
2.75-2.920.21461420.20232688X-RAY DIFFRACTION100
2.92-3.140.24031450.19732752X-RAY DIFFRACTION100
3.14-3.460.18741430.18482718X-RAY DIFFRACTION99.97
3.46-3.960.18661430.16742727X-RAY DIFFRACTION100
3.96-4.980.15441460.14932776X-RAY DIFFRACTION100
4.98-100.20261520.17432859X-RAY DIFFRACTION99.57

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