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- PDB-4zic: Crystal Structure of Aspartate Semialdehyde Dehydrogenase with NA... -

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Basic information

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


aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity / nucleus / cytosol
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 ...: / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesTrichophyton rubrum BMU01672 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.553 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 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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


Theoretical massNumber of molelcules
Total (without water)246,18314
Polymers244,1206
Non-polymers2,0638
Water9,782543
1
D: Aspartate Semialdehyde Dehydrogenase
C: Aspartate Semialdehyde Dehydrogenase
A: Aspartate Semialdehyde Dehydrogenase
B: Aspartate Semialdehyde Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,61810
Polymers162,7464
Non-polymers1,8716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14690 Å2
ΔGint-140 kcal/mol
Surface area47520 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)163,1318
Polymers162,7464
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area11750 Å2
ΔGint-97 kcal/mol
Surface area48340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.427, 157.427, 187.987
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11E-561-

HOH

21F-555-

HOH

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Components

#1: Protein
Aspartate Semialdehyde Dehydrogenase


Mass: 40686.613 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


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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 MGSSHHHHHHSSGLVPRGSHM 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.15M Ammonium Sulfate, 0.1M Sodium Citrate, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97876 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2014
RadiationMonochromator: Double Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 169359 / Num. obs: 168846 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.84 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 19.84
Reflection shellResolution: 2.55→2.71 Å / Redundancy: 3.83 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 4.37 / % possible all: 99.4

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Processing

SoftwareName: PHENIX / Version: 1.7.3_928 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZHS

4zhs


Resolution: 2.553→46.133 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.16 / 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% reflection
Rfree0.2725 4385 5.01 %
Rwork0.2267 --
obs0.229 87486 99.73 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.802 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3413 Å20 Å2-0 Å2
2--0.3413 Å2-0 Å2
3----0.6827 Å2
Refinement stepCycle: LAST / Resolution: 2.553→46.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16043 0 126 543 16712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416604
X-RAY DIFFRACTIONf_angle_d1.05622558
X-RAY DIFFRACTIONf_dihedral_angle_d13.0816171
X-RAY DIFFRACTIONf_chiral_restr0.0762580
X-RAY DIFFRACTIONf_plane_restr0.0042953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5527-2.58170.41061240.30732760X-RAY DIFFRACTION99
2.5817-2.61210.30181300.29432719X-RAY DIFFRACTION100
2.6121-2.64390.41321330.29232742X-RAY DIFFRACTION100
2.6439-2.67740.3381370.29042745X-RAY DIFFRACTION100
2.6774-2.71260.41211470.29472751X-RAY DIFFRACTION100
2.7126-2.74980.3741520.28972735X-RAY DIFFRACTION100
2.7498-2.78910.35391360.28192745X-RAY DIFFRACTION100
2.7891-2.83070.32231340.26532746X-RAY DIFFRACTION100
2.8307-2.87490.35031420.2772780X-RAY DIFFRACTION100
2.8749-2.9220.33711730.27922711X-RAY DIFFRACTION100
2.922-2.97240.30861430.27252767X-RAY DIFFRACTION100
2.9724-3.02640.35541520.29232757X-RAY DIFFRACTION100
3.0264-3.08460.31891430.26972753X-RAY DIFFRACTION100
3.0846-3.14760.30071460.26292751X-RAY DIFFRACTION100
3.1476-3.2160.31771480.26072760X-RAY DIFFRACTION100
3.216-3.29080.28241540.25192716X-RAY DIFFRACTION100
3.2908-3.37310.29711580.24642766X-RAY DIFFRACTION100
3.3731-3.46430.28861270.2362794X-RAY DIFFRACTION100
3.4643-3.56620.28441570.22782744X-RAY DIFFRACTION100
3.5662-3.68120.24251410.22592791X-RAY DIFFRACTION100
3.6812-3.81270.24621560.22432768X-RAY DIFFRACTION100
3.8127-3.96530.26661380.20822768X-RAY DIFFRACTION100
3.9653-4.14570.2131600.20092798X-RAY DIFFRACTION100
4.1457-4.36410.21711480.18092765X-RAY DIFFRACTION100
4.3641-4.63730.23431400.17842810X-RAY DIFFRACTION100
4.6373-4.99490.22341430.17372789X-RAY DIFFRACTION100
4.9949-5.49680.24541480.19162812X-RAY DIFFRACTION100
5.4968-6.29050.28921530.22222838X-RAY DIFFRACTION100
6.2905-7.91890.24581710.20322833X-RAY DIFFRACTION100
7.9189-46.14020.21251510.19682887X-RAY DIFFRACTION97

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