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- PDB-3fq8: M248I mutant of GSAM -

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Basic information

Entry
Database: PDB / ID: 3fq8
TitleM248I mutant of GSAM
ComponentsGlutamate-1-semialdehyde 2,1-aminomutase
KeywordsISOMERASE / Drug resistance / Microev0lution / Integrated approach / Chlorophyll biosynthesis / Cytoplasm / Porphyrin biosynthesis / Pyridoxal phosphate
Function / homology
Function and homology information


glutamate-1-semialdehyde 2,1-aminomutase / glutamate-1-semialdehyde 2,1-aminomutase activity / chlorophyll biosynthetic process / protoporphyrinogen IX biosynthetic process / transaminase activity / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Tetrapyrrole biosynthesis, glutamate-1-semialdehyde aminotransferase / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Tetrapyrrole biosynthesis, glutamate-1-semialdehyde aminotransferase / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Glutamate-1-semialdehyde 2,1-aminomutase
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 6301 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStetefeld, J.
CitationJournal: Faseb J. / Year: 2010
Title: Absence of a catalytic water confers resistance to the neurotoxin gabaculine.
Authors: Orriss, G.L. / Patel, T.R. / Sorensen, J. / Stetefeld, J.
History
DepositionJan 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate-1-semialdehyde 2,1-aminomutase
B: Glutamate-1-semialdehyde 2,1-aminomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6364
Polymers91,1402
Non-polymers4962
Water12,484693
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-56 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.680, 106.951, 122.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsGSAM is an alpha 2 dimer in solution. The asymetric unit contains one dimer.

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Components

#1: Protein Glutamate-1-semialdehyde 2,1-aminomutase / GSA / Glutamate-1-semialdehyde aminotransferase / GSA-AT


Mass: 45569.988 Da / Num. of mol.: 2 / Fragment: sequence database residues 7-433 / Mutation: M248I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 6301 (bacteria)
Gene: hemL, gsa, syc0881_c / Plasmid: PSAT 1.4 / Production host: Escherichia coli (E. coli) / Variant (production host): K74
References: UniProt: P24630, glutamate-1-semialdehyde 2,1-aminomutase
#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 6

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 273 K / Method: vapor diffusion / pH: 6.8 / Details: pH 6.8, VAPOR DIFFUSION, temperature 273K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.1154 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1154 Å / Relative weight: 1
ReflectionResolution: 2→28 Å / Num. obs: 56587 / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 7.5 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNS1.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HP2

2hp2


Resolution: 2→27.9 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2543494.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.245 5754 10.2 %RANDOM
Rwork0.208 ---
obs0.208 56587 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.407 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.7 Å20 Å20 Å2
2---4.41 Å20 Å2
3---0.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→27.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 32 693 7129
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 982 10.2 %
Rwork0.246 8609 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3pmp.param

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