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- PDB-4zhs: Crystal Structure of Aspartate Semialdehyde Dehydrogenase from Tr... -

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Basic information

Entry
Database: PDB / ID: 4zhs
TitleCrystal Structure of Aspartate Semialdehyde Dehydrogenase from Trichophyton rubrum
ComponentsAspartate Semialdehyde DehydrogenaseAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Aspartate-semialdehyde dehydrogenase / Trichophyton rubrum / tetramer
Function / homology
Function and homology information


aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity
Similarity search - Function
Aspartate-semialdehyde dehydrogenase, peptidoglycan lacking / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase signature. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 ...Aspartate-semialdehyde dehydrogenase, peptidoglycan lacking / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase signature. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesTrichophyton rubrum BMU01672 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.603 Å
AuthorsLi, Q. / Cui, S.
CitationJournal: Sci Rep / Year: 2016
Title: Structural Insights into the Tetrameric State of Aspartate-beta-semialdehyde Dehydrogenases from Fungal Species
Authors: Li, Q. / Mu, Z. / Zhao, R. / Dahal, G. / Viola, R.E. / Liu, T. / Jin, Q. / Cui, S.
History
DepositionApr 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Aspartate Semialdehyde Dehydrogenase
C: Aspartate Semialdehyde Dehydrogenase
B: Aspartate Semialdehyde Dehydrogenase
E: Aspartate Semialdehyde Dehydrogenase
A: Aspartate Semialdehyde Dehydrogenase
F: Aspartate Semialdehyde Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,79112
Polymers247,2156
Non-polymers5766
Water7,224401
1
D: Aspartate Semialdehyde Dehydrogenase
C: Aspartate Semialdehyde Dehydrogenase
B: Aspartate Semialdehyde Dehydrogenase
A: Aspartate Semialdehyde Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,1948
Polymers164,8104
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12010 Å2
ΔGint-129 kcal/mol
Surface area49450 Å2
MethodPISA
2
E: Aspartate Semialdehyde Dehydrogenase
F: Aspartate Semialdehyde Dehydrogenase
hetero molecules

E: Aspartate Semialdehyde Dehydrogenase
F: Aspartate Semialdehyde Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,1948
Polymers164,8104
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area11880 Å2
ΔGint-92 kcal/mol
Surface area48640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.504, 157.504, 188.401
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Aspartate Semialdehyde Dehydrogenase / Aspartate-semialdehyde dehydrogenase


Mass: 41202.453 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichophyton rubrum BMU01672 (fungus) / Strain: BMU01672 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: A0A140UHG6*PLUS, aspartate-semialdehyde dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. N-TERMINAL RESIDUES (MSE)GSSHHHHHHSSGLVPRGSH(MSE) ARE THE EXPRESSION TAGS.

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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: 2.73 Å3/Da / Density meas: 8 Mg/m3 / Density % sol: 54.93 % / Description: oblong shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.2M Ammonium Sulfate, 0.1M Sodium citrate pH5.4, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2014
RadiationMonochromator: Double Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→27.621 Å / Num. all: 320452 / Num. obs: 311564 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.87 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.24
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 1.56 / % possible all: 97.1

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Processing

SoftwareName: PHENIX / Version: 1.7.3_928 / Classification: refinement
RefinementResolution: 2.603→27.621 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6 / Stereochemistry target values: ML
Details: DURING DATA COLLECTION, F+ AND F- WERE CONSIDERED AS DIFFERENT REFLECTION BECAUSE THE FRIEDEL'S LAW WAS FALSE. AFTER MOLECULAR REPLACEMENT FOR STRUCTURE DETERMINATION, IN THE REFINEMENT F+ ...Details: DURING DATA COLLECTION, F+ AND F- WERE CONSIDERED AS DIFFERENT REFLECTION BECAUSE THE FRIEDEL'S LAW WAS FALSE. AFTER MOLECULAR REPLACEMENT FOR STRUCTURE DETERMINATION, IN THE REFINEMENT F+ AND F- WERE MERGED THEREFORE THE REFLECTION COUNTED WERE AROUND 50% OF DATA COLLECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 8002 5.02 %Random
Rwork0.2136 ---
obs0.2158 159440 99.57 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.619 Å2 / ksol: 0.299 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5371 Å2-0 Å2-0 Å2
2--1.5371 Å2-0 Å2
3----3.0743 Å2
Refinement stepCycle: LAST / Resolution: 2.603→27.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15812 0 30 401 16243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716139
X-RAY DIFFRACTIONf_angle_d1.05921883
X-RAY DIFFRACTIONf_dihedral_angle_d14.7795997
X-RAY DIFFRACTIONf_chiral_restr0.0532518
X-RAY DIFFRACTIONf_plane_restr0.0052875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6032-2.63270.34772470.30074792X-RAY DIFFRACTION95
2.6327-2.66370.34192540.31065130X-RAY DIFFRACTION100
2.6637-2.69610.35852440.30715097X-RAY DIFFRACTION100
2.6961-2.73020.35542530.3095068X-RAY DIFFRACTION100
2.7302-2.76610.34462950.29515049X-RAY DIFFRACTION100
2.7661-2.8040.33052680.27675025X-RAY DIFFRACTION100
2.804-2.8440.33882670.26675046X-RAY DIFFRACTION100
2.844-2.88640.29992560.26875101X-RAY DIFFRACTION100
2.8864-2.93140.31172620.27715109X-RAY DIFFRACTION100
2.9314-2.97940.31652580.26275072X-RAY DIFFRACTION100
2.9794-3.03080.32962500.28345102X-RAY DIFFRACTION100
3.0308-3.08580.35432230.27315085X-RAY DIFFRACTION100
3.0858-3.14510.29343030.25665010X-RAY DIFFRACTION100
3.1451-3.20920.30442570.25715098X-RAY DIFFRACTION100
3.2092-3.27890.26722800.24375090X-RAY DIFFRACTION100
3.2789-3.3550.2742500.23755059X-RAY DIFFRACTION100
3.355-3.43870.26942790.22685041X-RAY DIFFRACTION100
3.4387-3.53150.27712540.22365056X-RAY DIFFRACTION100
3.5315-3.63520.28412500.21375069X-RAY DIFFRACTION100
3.6352-3.75230.25542880.21315089X-RAY DIFFRACTION100
3.7523-3.88610.27472520.20155031X-RAY DIFFRACTION100
3.8861-4.04120.22122910.18665094X-RAY DIFFRACTION100
4.0412-4.22450.19953060.1634964X-RAY DIFFRACTION100
4.2245-4.44640.19452920.15915048X-RAY DIFFRACTION100
4.4464-4.72370.21072790.15785085X-RAY DIFFRACTION100
4.7237-5.08630.19882830.16525020X-RAY DIFFRACTION100
5.0863-5.59430.2452650.18165065X-RAY DIFFRACTION100
5.5943-6.3950.25382520.20645033X-RAY DIFFRACTION100
6.395-8.02420.23252850.1875074X-RAY DIFFRACTION100
8.0242-27.62290.21692590.19144836X-RAY DIFFRACTION95

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