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- PDB-6w80: Crystal structure of Glutamate-1-semialdehyde 2,1-aminomutase fro... -

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Basic information

Entry
Database: PDB / ID: 6w80
TitleCrystal structure of Glutamate-1-semialdehyde 2,1-aminomutase from Stenotrophomonas maltophilia K279a in complex with PLP
ComponentsGlutamate-1-semialdehyde 2,1-aminomutase
KeywordsISOMERASE / SSGCID / Stenotrophomonas maltophilia / Glutamate-1-semialdehyde 2 / 1-aminomutase / hemL / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glutamate-1-semialdehyde 2,1-aminomutase / glutamate-1-semialdehyde 2,1-aminomutase activity / 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
PYRIDOXAL-5'-PHOSPHATE / Glutamate-1-semialdehyde 2,1-aminomutase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Glutamate-1-semialdehyde 2,1-aminomutase from Stenotrophomonas maltophilia K279a in complex with PLP
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,3892
Polymers46,1411
Non-polymers2471
Water9,386521
1
A: Glutamate-1-semialdehyde 2,1-aminomutase
hetero molecules

A: Glutamate-1-semialdehyde 2,1-aminomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7774
Polymers92,2832
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area10180 Å2
ΔGint-53 kcal/mol
Surface area26670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.280, 60.280, 367.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-832-

HOH

21A-899-

HOH

31A-951-

HOH

41A-965-

HOH

51A-1114-

HOH

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Components

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


Mass: 46141.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: hemL, Smlt3873 / Plasmid: StmaA.01026.c.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: B2FT35, glutamate-1-semialdehyde 2,1-aminomutase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 13.4 mg/mL StmaA.01026.c.B1.PW38743 + 2 mM PLP + 2 mM alanine against Molecular Dimensions Morpheus screen, condition g9 (10% w/V PEG20000, 20% V/V PEG550 MME, 20 mM sodium formate, 20 mM ...Details: 13.4 mg/mL StmaA.01026.c.B1.PW38743 + 2 mM PLP + 2 mM alanine against Molecular Dimensions Morpheus screen, condition g9 (10% w/V PEG20000, 20% V/V PEG550 MME, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium citrate, 20 mM sodium potassium l-tartrate, 20 mM sodium oxamate, 100 mM Bicine/Trizma base, pH 8.5), direct cryoprotection, tray: 313929g9, puck jxa1-2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 12, 2020
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 79730 / % possible obs: 99.8 % / Redundancy: 10.338 % / Biso Wilson estimate: 23.293 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.062 / Χ2: 1.097 / Net I/σ(I): 20.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.449.9280.6253.3158000.8730.659100
1.44-1.4810.6360.4874.4955890.9210.512100
1.48-1.5210.6180.3785.8454680.9570.397100
1.52-1.5710.6470.3077.2153000.9710.322100
1.57-1.6210.6640.2359.451700.9850.247100
1.62-1.6710.670.19811.3350450.9890.208100
1.67-1.7410.6840.16113.8348200.9920.169100
1.74-1.8110.6310.13416.8446740.9940.141100
1.81-1.8910.6380.11120.2245250.9960.117100
1.89-1.9810.5360.09124.6742780.9970.096100
1.98-2.0910.4160.07728.6341460.9970.081100
2.09-2.2110.3130.06731.6839000.9980.071100
2.21-2.3710.210.06233.836950.9980.065100
2.37-2.5610.1270.05636.4334560.9980.059100
2.56-2.810.0650.05138.6632110.9990.05499.9
2.8-3.139.9860.04640.2729340.9990.04999.9
3.13-3.619.8640.04342.0126170.9990.04599.9
3.61-4.439.6010.03942.1222670.9990.04199.8
4.43-6.269.2990.03541.6718190.9990.03799.6
6.26-507.0420.03735.5710160.9980.0487.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5i92 chain A as per MORDA

5i92


Resolution: 1.4→34.47 Å / SU ML: 0.124 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.1634
RfactorNum. reflection% reflectionSelection details
Rfree0.1814 1933 2.43 %0
Rwork0.1344 ---
obs0.1355 79539 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.89 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 0 521 3711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083390
X-RAY DIFFRACTIONf_angle_d1.03254631
X-RAY DIFFRACTIONf_chiral_restr0.0893513
X-RAY DIFFRACTIONf_plane_restr0.0073633
X-RAY DIFFRACTIONf_dihedral_angle_d19.80181237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.2161590.16455425X-RAY DIFFRACTION100
1.44-1.470.23391350.14775398X-RAY DIFFRACTION100
1.47-1.520.1951470.13215395X-RAY DIFFRACTION100
1.52-1.570.17941330.11955433X-RAY DIFFRACTION100
1.57-1.620.17321380.1115478X-RAY DIFFRACTION100
1.62-1.690.18751390.11285453X-RAY DIFFRACTION100
1.69-1.760.18181150.1175509X-RAY DIFFRACTION100
1.76-1.860.19951340.12155467X-RAY DIFFRACTION100
1.86-1.970.17451370.12425527X-RAY DIFFRACTION100
1.97-2.130.18291440.12755547X-RAY DIFFRACTION100
2.13-2.340.1841420.13175581X-RAY DIFFRACTION100
2.34-2.680.17411220.14015634X-RAY DIFFRACTION99.98
2.68-3.370.17551280.14285769X-RAY DIFFRACTION99.98
3.37-34.470.17741600.14075990X-RAY DIFFRACTION98.01

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