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- PDB-1brm: ASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1brm
TitleASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE FROM ESCHERICHIA COLI
ComponentsASPARTATE-SEMIALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / ESCHERICHIA COLI / ENZYME / NADP
Function / homology
Function and homology information


homoserine biosynthetic process / 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 ...homoserine biosynthetic process / 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 / DNA damage response / cytosol
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
Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.5 Å
AuthorsHadfield, A.T. / Kryger, G. / Ouyang, J. / Ringe, D. / Petsko, G.A. / Viola, R.E.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structure of aspartate-beta-semialdehyde dehydrogenase from Escherichia coli, a key enzyme in the aspartate family of amino acid biosynthesis.
Authors: Hadfield, A. / Kryger, G. / Ouyang, J. / Petsko, G.A. / Ringe, D. / Viola, R.
History
DepositionAug 24, 1998Processing site: BNL
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASPARTATE-SEMIALDEHYDE DEHYDROGENASE
B: ASPARTATE-SEMIALDEHYDE DEHYDROGENASE
C: ASPARTATE-SEMIALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)120,1703
Polymers120,1703
Non-polymers00
Water5,459303
1
A: ASPARTATE-SEMIALDEHYDE DEHYDROGENASE
B: ASPARTATE-SEMIALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)80,1132
Polymers80,1132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-51 kcal/mol
Surface area26520 Å2
MethodPISA
2
C: ASPARTATE-SEMIALDEHYDE DEHYDROGENASE

C: ASPARTATE-SEMIALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)80,1132
Polymers80,1132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)174.890, 117.050, 58.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.331583, 0.519701, -0.787378), (0.534861, -0.583953, -0.610674), (-0.77716, -0.623626, -0.084339)74.47873, 6.9576, 68.36593
2given(-0.798346, 0.165907, -0.578895), (0.156914, -0.870783, -0.465956), (-0.581397, -0.462831, 0.669153)136.04611, 71.52384, 67.39461

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Components

#1: Protein ASPARTATE-SEMIALDEHYDE DEHYDROGENASE / / ASADH / ASDH


Mass: 40056.738 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ASD / Plasmid: PGEM / Cell line (production host): JM109 / Gene (production host): ASD / Production host: Escherichia coli (E. coli)
References: UniProt: P0A9Q9, aspartate-semialdehyde dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.48 Å3/Da / Density % sol: 50 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlenzyme1drop
210 mMHEPES1drop
31 mMdithiothreitol1drop
41 MEDTA1drop
51 mM1dropNaN3
619 %PEG40001reservoir
70.35 M1reservoirMgCl2
80.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.0098
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0098 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 37745 / % possible obs: 79.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 15.8
Reflection shellResolution: 2.49→2.59 Å / Rmerge(I) obs: 0.177 / Rsym value: 0.177 / % possible all: 59.9
Reflection
*PLUS
% possible obs: 86 % / Num. measured all: 116166 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 59.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.85model building
X-PLOR3.85refinement
HKLdata reduction
HKLdata scaling
X-PLOR3.85phasing
RefinementMethod to determine structure: SIR / Resolution: 2.5→28 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.294 -10 %
Rwork0.225 --
obs0.225 34798 82.6 %
Displacement parametersBiso mean: 39 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8199 0 0 303 8502
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.19
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.436 -10 %
Rwork0.401 2731 -
obs--58.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 33159 / Num. reflection Rfree: 3466 / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.18

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