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- PDB-3gsb: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE IN COMP... -

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Basic information

Entry
Database: PDB / ID: 3gsb
TitleCRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE IN COMPLEX WITH GABACULINE
ComponentsPROTEIN (GLUTAMATE SEMIALDEHYDE AMINOTRANSFERASE)
KeywordsISOMERASE / CHLOROPHYLL BIOSYNTHESIS / PYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE / ASYMMETRIC DIMER / GABACULINE
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
3-AMINOBENZOIC ACID / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Glutamate-1-semialdehyde 2,1-aminomutase
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3 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
DepositionJun 26, 1998Deposition site: BNL / Processing site: RCSB
SupersessionAug 17, 1999ID: 3GSA
Revision 1.0Aug 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: 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: PROTEIN (GLUTAMATE SEMIALDEHYDE AMINOTRANSFERASE)
B: PROTEIN (GLUTAMATE SEMIALDEHYDE AMINOTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7535
Polymers92,1192
Non-polymers6333
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint-50 kcal/mol
Surface area25600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.600, 108.600, 123.500
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 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.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical ChemComp-GAB / 3-AMINOBENZOIC ACID / GABACULINE


Mass: 137.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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 WATERS WERE REMOVED FROM THE MODEL
Crystal growpH: 7
Details: 50MM NA-CACODYLATE BUFFER PH 7.0, 200 MM MG-ACETATE, 19.5% PEG 10,000, SOAKING CONDITIONS: 3MM GABACULINE FOR 4 DAYS
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
619.5 %PEG100001reservoir

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 18, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. obs: 18662 / % possible obs: 98 % / Redundancy: 3.1 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.114 / Net I/σ(I): 6.2
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.412 / % possible all: 96.4
Reflection
*PLUS
Num. measured all: 57653 / Rmerge(I) obs: 0.114

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementStarting model: GSAT WILD-TYPE (NATIVE) STRUCTURE

Resolution: 3→15 Å
RfactorNum. reflection% reflection
Rfree0.25 -5 %
Rwork0.159 --
obs0.159 18662 98 %
Displacement parametersBiso mean: 29.6 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 42 157 6601
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.98
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: 3→3.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 39 5 %
Rwork0.28 811 -
obs--96.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_mcbond_it3
X-RAY DIFFRACTIONx_scbond_it6
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it3
LS refinement shell
*PLUS
Rfactor Rfree: 0.38 / % reflection Rfree: 5 % / Rfactor Rwork: 0.28

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