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- PDB-8bj1: Crystal structure of Medicago truncatula histidinol-phosphate ami... -

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Basic information

Entry
Database: PDB / ID: 8bj1
TitleCrystal structure of Medicago truncatula histidinol-phosphate aminotransferase (HISN6) in the open state
Componentshistidinol-phosphate aminotransferase
KeywordsTRANSFERASE / HISN6 / histidinol-phosphate aminotransferase / aminotransferase / plant / open
Function / homology
Function and homology information


histidinol-phosphate transaminase / histidinol-phosphate transaminase activity / L-histidine biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Histidinol-phosphate aminotransferase family / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
histidinol-phosphate transaminase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsRutkiewicz, M. / Ruszkowski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2018/31/D/NZ1/03630 Poland
CitationJournal: Plant Physiol Biochem. / Year: 2023
Title: Insights into the substrate specificity, structure, and dynamics of plant histidinol-phosphate aminotransferase (HISN6).
Authors: Rutkiewicz, M. / Nogues, I. / Witek, W. / Angelaccio, S. / Contestabile, R. / Ruszkowski, M.
History
DepositionNov 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: histidinol-phosphate aminotransferase
B: histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,97325
Polymers81,4202
Non-polymers1,55323
Water15,169842
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-111 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.661, 87.373, 74.235
Angle α, β, γ (deg.)90.000, 95.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein histidinol-phosphate aminotransferase


Mass: 40710.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A072U7F9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 842 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate; 0.1 M MES pH 6.5; 30 % w/v PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→36.97 Å / Num. obs: 116740 / % possible obs: 98.6 % / Redundancy: 3.879 % / Biso Wilson estimate: 20.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.052 / Χ2: 1.116 / Net I/σ(I): 18.02 / Num. measured all: 452887
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.57-1.663.850.6671.867258219123188530.6560.77798.6
1.66-1.783.9020.3963.376932817878177690.8620.46199.4
1.78-1.923.7960.2236.096183716695162910.950.2697.6
1.92-2.13.9410.12211.165960115374151220.9860.14298.4
2.1-2.353.960.071195489913932138650.9950.08299.5
2.35-2.723.7730.04626.764557212302120800.9970.05498.2
2.72-3.333.9690.02940.464100310438103300.9990.03399
3.33-4.73.9130.0257.4831262806479900.9990.02399.1
4.7-36.973.7840.01862.3716803453544400.9990.0297.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3euc

3euc


Resolution: 1.57→36.97 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1699 1167 1 %
Rwork0.1274 115563 -
obs0.1278 116730 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.38 Å2 / Biso mean: 28.2775 Å2 / Biso min: 12.82 Å2
Refinement stepCycle: final / Resolution: 1.57→36.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5713 0 92 886 6691
Biso mean--44.81 43.62 -
Num. residues----719
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.57-1.640.26761450.2027143811452698
1.64-1.730.27911470.17371450414651100
1.73-1.840.17141450.1268144071455299
1.84-1.980.16741430.111140961423996
1.98-2.180.17661470.10361456214709100
2.18-2.490.14531470.1075145811472899
2.49-3.140.18581450.1305143601450598
3.14-36.970.151480.132146721482099

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