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- PDB-1pqp: Crystal Structure of the C136S Mutant of Aspartate Semialdehyde D... -

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Basic information

Entry
Database: PDB / ID: 1pqp
TitleCrystal Structure of the C136S Mutant of Aspartate Semialdehyde Dehydrogenase from Haemophilus influenzae Bound with Aspartate Semialdehyde and Phosphate
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Enzyme / L-aspartate semialdehyde / L-aspartate semialdehyde dehydrogenase / phosphate
Function / homology
Function and homology information


aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / isoleucine biosynthetic process / diaminopimelate 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
L-HOMOSERINE / PHOSPHATE ION / Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHaemophilus influenzae Rd (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsBlanco, J. / Moore, R.A. / Faehnle, C.R. / Viola, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: The role of substrate-binding groups in the mechanism of aspartate-beta-semialdehyde dehydrogenase.
Authors: Blanco, J. / Moore, R.A. / Faehnle, C.R. / Coe, D.M. / Viola, R.E.
History
DepositionJun 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7823
Polymers40,5681
Non-polymers2142
Water3,873215
1
A: Aspartate-semialdehyde dehydrogenase
hetero molecules

A: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5646
Polymers81,1352
Non-polymers4284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area7860 Å2
ΔGint-55 kcal/mol
Surface area26380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)113.949, 55.059, 57.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer.

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Components

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


Mass: 40567.672 Da / Num. of mol.: 1 / Mutation: C136S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd (bacteria) / Species: Haemophilus influenzae / Strain: KW20 / Gene: asd / Plasmid: PET43 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P44801, aspartate-semialdehyde dehydrogenase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-HSE / L-HOMOSERINE / Homoserine


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% PEG 3350, 0.2M Ammonium acetate, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jul 18, 2002
RadiationMonochromator: Si220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 27514 / Num. obs: 27474 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Biso Wilson estimate: 10.9 Å2 / Rsym value: 0.049 / Net I/σ(I): 29.7
Reflection shellResolution: 1.91→1.98 Å / Mean I/σ(I) obs: 13.4 / Num. unique all: 2447 / Rsym value: 0.118 / % possible all: 85.8

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Processing

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

1nwc


Resolution: 2.06→37.64 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2143 9.8 %RANDOM
Rwork0.228 ---
all0.236 23196 --
obs0.228 21902 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.9707 Å2 / ksol: 0.371209 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1--9.2 Å20 Å20 Å2
2--3.67 Å20 Å2
3---5.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.06→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 13 215 2981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.06→2.19 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 346 9.4 %
Rwork0.229 3347 -
obs-3347 97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PI.PARAMPI.TOP
X-RAY DIFFRACTION3ASA.PARAMASA.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP

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