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- PDB-2gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE (AMINOT... -

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Basic information

Entry
Database: PDB / ID: 2gsa
TitleCRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE (AMINOTRANSFERASE, WILD-TYPE FORM)
ComponentsGLUTAMATE SEMIALDEHYDE AMINOTRANSFERASE
KeywordsCHLOROPHYLL BIOSYNTHESIS / PYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE / ASYMMETRIC DIMER
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
PYRIDOXAL-5'-PHOSPHATE / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Glutamate-1-semialdehyde 2,1-aminomutase
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsHennig, M. / Jansonius, J.N.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Crystal structure of glutamate-1-semialdehyde aminomutase: an alpha2-dimeric vitamin B6-dependent enzyme with asymmetry in structure and active site reactivity.
Authors: Hennig, M. / Grimm, B. / Contestabile, R. / John, R.A. / Jansonius, J.N.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Analysis of Wild-Type and K272A Mutant Glutamate 1-Semialdehyde Aminotransferase from Synechococcus
Authors: Hennig, M. / Grimm, B. / Jenny, M. / Muller, R. / Jansonius, J.N.
History
DepositionFeb 26, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jun 5, 2024Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: GLUTAMATE SEMIALDEHYDE AMINOTRANSFERASE
B: GLUTAMATE SEMIALDEHYDE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6144
Polymers92,1192
Non-polymers4952
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-57 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.620, 108.600, 122.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE ASYMMETRIC UNIT CONTAINS A STRUCTURALLY ASYMMETRIC HOMODIMER.

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Components

#1: Protein GLUTAMATE SEMIALDEHYDE AMINOTRANSFERASE / GLUTAMATE SEMIALDEHYDE AMINOMUTASE


Mass: 46059.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: GR6 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009
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.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growpH: 7
Details: 50MM NA-CACODYLATE BUFFER PH 7.0, 200 MM MG-ACETATE, 19.5% PEG 10,000
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / Details: Hennig, M., (1994) J.Mol.Biol., 242, 591.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.6-6 mg/mlprotein1drop
230 mMsodium cacodylate1drop
380 mMmagnesium acetate1drop
47.8 %PEG100001drop
5200 mMmagnesium acetate1reservoir
619.5PEG100001reservoir

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 12, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 34132 / % possible obs: 94.6 % / Redundancy: 3.25 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.068 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.52 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.3 / % possible all: 92.2
Reflection
*PLUS
Num. measured all: 110780 / Rmerge(I) obs: 0.068

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→10 Å
Details: RESIDUES FROM HIS 153 TO THR 181 ARE DISORDERED AND HAVE OCCUPANCY 0.0.
RfactorNum. reflection% reflection
Rfree0.25 -5 %
Rwork0.183 --
obs0.183 34132 94.2 %
Displacement parametersBiso mean: 29.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 31 347 6780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.76
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_it3
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it6
X-RAY DIFFRACTIONx_scangle_it3
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.39 201 5 %
Rwork0.33 3831 -
obs--94.9 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS

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