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- PDB-3usf: Crystal structure of DAVA-4 -

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Basic information

Entry
Database: PDB / ID: 3usf
TitleCrystal structure of DAVA-4
ComponentsGlutamate-1-semialdehyde 2,1-aminomutase
KeywordsISOMERASE / shuttle movement of non-cofactor bound intermediates
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 / Pyridoxal phosphate-dependent transferase, major 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
(4S)-4,5-DIAMINOPENTANOIC ACID / Chem-PLR / Glutamate-1-semialdehyde 2,1-aminomutase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.463 Å
AuthorsStetefeld, J.
CitationJournal: To be Published
Title: Crystal structure of DAVA-4
Authors: Stetefeld, J.
History
DepositionNov 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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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)91,7755
Polymers91,1762
Non-polymers5983
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-49 kcal/mol
Surface area26660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.582, 108.781, 124.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 45588.023 Da / Num. of mol.: 2 / Fragment: UNP residues 7-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Production host: Escherichia coli (E. coli)
References: UniProt: Q31QJ2, glutamate-1-semialdehyde 2,1-aminomutase
#2: Chemical ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12NO5P
#3: Chemical ChemComp-HOZ / (4S)-4,5-DIAMINOPENTANOIC ACID


Mass: 132.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.55 Å3/Da / Density % sol: 51.79 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9874 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9874 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 31835 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 28.7 Å2

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Processing

Software
NameVersionClassificationNB
CNS1.3refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.463→8 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 3159974 / 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
Rfree0.232 3125 10 %RANDOM
Rwork0.178 ---
obs-31267 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.4315 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso max: 76.98 Å2 / Biso mean: 28.4893 Å2 / Biso min: 5.92 Å2
Baniso -1Baniso -2Baniso -3
1-7.27 Å20 Å20 Å2
2---6.17 Å20 Å2
3----1.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.463→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6234 0 39 327 6600
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.463→2.55 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 243 10.6 %
Rwork0.239 2048 -
all-2291 -
obs--38.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6plp.parplp.top
X-RAY DIFFRACTION7dav.pardav.top

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