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- PDB-1gl3: ASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE IN COMPLEX WITH NADP AN... -

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Basic information

Entry
Database: PDB / ID: 1gl3
TitleASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE IN COMPLEX WITH NADP AND SUBSTRATE ANALOGUE S-METHYL CYSTEINE SULFOXIDE
ComponentsASPARTATE-SEMIALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / ESCHERICHIA COLI / ENZYME / NADP / DIAMINOPIMELATE BIOSYNTHESI LYSINE BIOSYNTHESIS
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
CYSTEINE / Chem-NDP / Aspartate-semialdehyde dehydrogenase / Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHadfield, A.T. / Kryger, G. / Ouyang, J. / Ringe, D. / Petsko, G.A. / Viola, R.E.
Citation
Journal: Biochemistry / Year: 2001
Title: Active Site Analysis of the Potential Antimicrobial Target Aspartate Semialdehyde Dehydrogenase.
Authors: Hadfield, A.T. / Shammas, C. / Kryger, G. / Ringe, D. / Petsko, G.A. / Ouyang, J. / Viola, R.E.
#1: Journal: 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.T. / Kryger, G. / Ouyang, J. / Petsko, G.A. / Viola, R.E.
History
DepositionAug 23, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7255
Polymers80,1132
Non-polymers1,6123
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)121.000, 121.000, 94.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9746, 0.224, -0.0013), (0.2239, 0.9745, 0.0112), (0.0038, 0.0106, -1)
Vector: 0.49, -0.46, 63.1)

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Components

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


Mass: 40056.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cell line: JM109 / Plasmid: PGEM / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): JM109
References: UniProt: P00353, UniProt: P0A9Q9*PLUS, aspartate-semialdehyde dehydrogenase
#2: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.75 Å3/Da / Density % sol: 55 %
Crystal growpH: 4.6
Details: RESERVOIR: 19% PEG 4K, 0.35M MGCL2, 0.2 M NH4AC 0.1M TRIS, pH 4.60
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1drop
21 mMdithiothreitol1drop
31 mMEDTA1drop
41 mM1droppH7.0NaN3
519 %PEG40001reservoir
60.35 M1reservoirMgCl2
70.2 Mammonium acetate1reservoir
80.1 Macetate1reservoirpH4.6
95 mMNADP1reservoir
102 mMSMCS1reservoir
1110 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 15, 1996
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→28 Å / Num. obs: 41666 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.103
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 1.5 / % possible all: 61.6
Reflection
*PLUS
Num. obs: 22099 / Num. measured all: 41666
Reflection shell
*PLUS
% possible obs: 61.6 %

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Processing

Software
NameVersionClassification
X-PLOR3.85refinement
XDSdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BRM
Resolution: 2.6→28 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 918 5 %RANDOM
Rwork0.2 ---
obs0.2 22099 96.3 %-
Displacement parametersBiso mean: 29.1 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5620 0 103 171 5894
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.32
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
LS refinement shellResolution: 2.6→2.74 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.409 50 5 %
Rwork0.309 2731 -
obs--61.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.NADPTOP.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.3 Å2

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