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- PDB-2r00: crystal structure of aspartate semialdehyde dehydrogenase II comp... -

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Basic information

Entry
Database: PDB / ID: 2r00
Titlecrystal structure of aspartate semialdehyde dehydrogenase II complexed with ASA from vibrio cholerae
Components(Aspartate-semialdehyde dehydrogenase) x 2
KeywordsOXIDOREDUCTASE / aspartate semialdehyde dehydrogenase / conformational change / half-of-sites-reactivity / protein evolution / sequence homology / subunit communication / Amino-acid biosynthesis / Diaminopimelate biosynthesis / Lysine biosynthesis / NADP
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, beta-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, beta-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
2,2'-oxydiacetic acid / Aspartate-semialdehyde dehydrogenase 2
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsViola, R.E. / Liu, X. / Ohren, J.F. / Faehnle, C.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: The structure of a redundant enzyme: a second isoform of aspartate beta-semialdehyde dehydrogenase in Vibrio cholerae.
Authors: Viola, R.E. / Liu, X. / Ohren, J.F. / Faehnle, C.R.
History
DepositionAug 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_special_symmetry / struct_conn / 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_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
B: Aspartate-semialdehyde dehydrogenase
C: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0854
Polymers111,9513
Non-polymers1341
Water10,809600
1
A: Aspartate-semialdehyde dehydrogenase
B: Aspartate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)74,5562
Polymers74,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-22.4 kcal/mol
Surface area25310 Å2
MethodPISA
2
C: Aspartate-semialdehyde dehydrogenase
hetero molecules

C: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0584
Polymers74,7902
Non-polymers2682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4640 Å2
ΔGint-26.8 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.376, 84.679, 114.976
Angle α, β, γ (deg.)90.00, 102.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-556-

HOH

21C-544-

HOH

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Components

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


Mass: 37277.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: E1 Tor / Gene: asd / Plasmid: pET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P23247, aspartate-semialdehyde dehydrogenase
#2: Protein Aspartate-semialdehyde dehydrogenase / ASA dehydrogenase / ASADH


Mass: 37394.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: E1 Tor / Gene: asd / Plasmid: pET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P23247, aspartate-semialdehyde dehydrogenase
#3: Chemical ChemComp-OEG / 2,2'-oxydiacetic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M sodium citrate pH 5.5, 27% PEG8000, 0.3M ammonium acetate, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 73968 / Num. obs: 70525 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rsym value: 0.053 / Net I/σ(I): 27
Reflection shellHighest resolution: 2 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5 / Rsym value: 0.33 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YS4

1ys4


Resolution: 2.03→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.746 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23237 3747 5 %RANDOM
Rwork0.19112 ---
obs0.19319 70525 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.037 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å20.41 Å2
2---0.11 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.03→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7383 0 9 600 7992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227538
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.93710249
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9425935
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.624.974380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8151202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2631543
X-RAY DIFFRACTIONr_chiral_restr0.0860.21156
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025836
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.23538
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.25131
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2579
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.299
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6911.54844
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15227589
X-RAY DIFFRACTIONr_scbond_it1.61633065
X-RAY DIFFRACTIONr_scangle_it2.534.52660
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.026→2.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 294 -
Rwork0.225 4969 -
obs--96.01 %

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