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- PDB-1nx6: Crystal Structure of Aspartate Semialdehyde Dehydrogenase from Ha... -

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Basic information

Entry
Database: PDB / ID: 1nx6
TitleCrystal Structure of Aspartate Semialdehyde Dehydrogenase from Haemophilus influenzae as a Tetrahedral Hemithiocetal Reaction intermediate with Phosphate at 2.15 A
ComponentsAspartate-Semialdehyde Dehydrogenase
KeywordsOXIDOREDUCTASE / aspartate-semialdehyde dehydrogenase / aspartate semialdehyde / Haemophilus influenzae / tetrahedal intermediate / hemithiocetal / phosphate
Function / homology
Function and homology information


aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / isoleucine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity
Similarity search - Function
Aspartate-semialdehyde dehydrogenase, gamma-type / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase / 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, gamma-type / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase / 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
PHOSPHATE ION / Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBlanco, J. / Moore, R.A. / Viola, R.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Capture of an Intermediate in the Catalytic Cycle of L-Aspartate-beta-Semialdehyde Dehydrogenase
Authors: Blanco, J. / Moore, R.A. / Viola, R.E.
History
DepositionFeb 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate-Semialdehyde Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8913
Polymers40,7011
Non-polymers1902
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aspartate-Semialdehyde Dehydrogenase
hetero molecules

A: Aspartate-Semialdehyde Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7826
Polymers81,4022
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area7790 Å2
ΔGint-77 kcal/mol
Surface area26730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)113.748, 54.853, 57.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a monomer

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Components

#1: Protein Aspartate-Semialdehyde Dehydrogenase / ASA dehydrogenase / ASADH


Mass: 40700.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: asd / Plasmid: PET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: P44801, aspartate-semialdehyde dehydrogenase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 43.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20-24% PEG 3350, 0.2 M Ammonium Acetate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
210 mMHEPES1drop
31 mMEDTA1drop
41 mMdithiothreitol1droppH7.0
524-28 %PEG33501reservoir
60.2 Mammonium acetate1reservoir
70.1 MTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2002
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→100 Å / Num. all: 20308 / Num. obs: 19724 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.06 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 27.8
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 5.6 / Num. unique all: 1992 / % possible all: 99.9
Reflection
*PLUS
% possible obs: 99.9 % / Num. measured all: 143627
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NWH

1nwh


Resolution: 2.15→40.5 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 280448.71 / Data cutoff high rms absF: 280448.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1945 9.9 %RANDOM
Rwork0.228 ---
all0.254 20283 --
obs0.228 19724 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.3946 Å2 / ksol: 0.312921 e/Å3
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1--12.52 Å20 Å20 Å2
2--4.29 Å20 Å2
3---8.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.15→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 10 144 2915
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.71
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 322 10.4 %
Rwork0.283 2780 -
obs-2780 93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_NEW.PARAMPROTEIN_NEW.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3PI.PARAMPI.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.71

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