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- PDB-4gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE (AMINOT... -

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Basic information

Entry
Database: PDB / ID: 4gsa
TitleCRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE (AMINOTRANSFERASE) REDUCED WITH CYANOBOROHYDRATE
ComponentsGLUTAMATE SEMIALDEHYDE AMINOTRANSFERASE
KeywordsCHLOROPHYLL BIOSYNTHESIS / PYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE / ASYMMETRIC DIMER / REDUCED FORM
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 / Glutamate-1-semialdehyde 2,1-aminomutase
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 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 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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)92,6134
Polymers92,1192
Non-polymers4942
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10380 Å2
ΔGint-57 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.640, 108.280, 122.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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 %
Description: COFACTORS AND WATER MOLECULES WERE REJECTED FROM THE MODEL.
Crystal growpH: 7
Details: 50MM NA-CACODYLATE BUFFER PH 7.0, 200 MM MG-ACETATE, 19.5% PEG 10,000
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
619.5 %PEG100001reservoir

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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: Apr 7, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 31141 / % possible obs: 96.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.073 / Net I/σ(I): 9.7
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2 / Rsym value: 37.2 / % possible all: 91.7
Reflection
*PLUS
Num. measured all: 91742 / Rmerge(I) obs: 0.073

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLOR3.1phasing
RefinementStarting model: GSAT WILD-TYPE STRUCTURE

Resolution: 2.5→15 Å
RfactorNum. reflection% reflection
Rfree0.264 -5 %
Rwork0.187 --
obs0.187 31141 96.8 %
Displacement parametersBiso mean: 28.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 30 190 6622
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.85
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: 2.5→2.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 59 5 %
Rwork0.32 1215 -
obs--92.4 %

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