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- PDB-8bj2: Crystal structure of Medicago truncatula histidinol-phosphate ami... -

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Basic information

Entry
Database: PDB / ID: 8bj2
TitleCrystal structure of Medicago truncatula histidinol-phosphate aminotransferase (HISN6) in the closed state
Componentshistidinol-phosphate aminotransferase
KeywordsTRANSFERASE / HISN6 / histidinol-phosphate aminotransferase / aminotransferase / plant / closed
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
ACETATE ION / histidinol-phosphate transaminase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 1.1May 1, 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)82,0618
Polymers81,4202
Non-polymers6416
Water18,9881054
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-56 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.935, 105.837, 66.487
Angle α, β, γ (deg.)90.000, 108.900, 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1054 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium acetate; 0.1M BIS_TRIS pH 6.5; 25% w/v polyethylene glycol 3350

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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: 1.4→53.86 Å / Num. obs: 145641 / % possible obs: 99.2 % / Redundancy: 4.027 % / Biso Wilson estimate: 16.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.058 / Χ2: 1.044 / Net I/σ(I): 13.89 / Num. measured all: 586491
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
1.4-1.483.6840.6621.898324323658225960.7320.7795.5
1.48-1.583.9320.3883.528774622332223180.8860.4599.9
1.58-1.714.0550.236.038394920728207040.9550.26699.9
1.71-1.884.1940.13110.427994519079190610.9860.1599.9
1.88-2.14.1820.07616.677216017272172550.9940.08899.9
2.1-2.424.1360.05324.076304515267152440.9970.0699.8
2.42-2.964.110.04229.115305212935129090.9980.04899.8
2.96-4.194.0480.03434.19404711002199990.9980.03999.8
4.19-53.864.1190.03136.9222879559355540.9980.03699.3

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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: MtHISN6_open

Resolution: 1.4→53.86 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1638 1164 0.8 %
Rwork0.1343 144463 -
obs0.1345 145627 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.57 Å2 / Biso mean: 21.2318 Å2 / Biso min: 11.77 Å2
Refinement stepCycle: final / Resolution: 1.4→53.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5720 0 40 1087 6847
Biso mean--32.83 32.95 -
Num. residues----720
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 (%)
1.4-1.460.28861370.2214170861722394
1.46-1.540.20531470.15871816918316100
1.54-1.630.19691460.13471812618272100
1.63-1.760.17441470.12381819218339100
1.76-1.940.1521460.11371812218268100
1.94-2.220.14921470.11371821918366100
2.22-2.80.14961470.13071821018357100
2.8-53.860.16021470.14021833918486100

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