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- PDB-8bj4: Crystal structure of Medicago truncatula histidinol-phosphate ami... -

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Basic information

Entry
Database: PDB / ID: 8bj4
TitleCrystal structure of Medicago truncatula histidinol-phosphate aminotransferase (HISN6) in apo form
Componentshistidinol-phosphate aminotransferase
KeywordsTRANSFERASE / HISN6 / histidinol-phosphate aminotransferase / aminotransferase / plant / apo
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 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
histidinol-phosphate transaminase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsRutkiewicz, M. / Witek, W. / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)166,16948
Polymers163,0174
Non-polymers3,15344
Water28,7881598
1
A: histidinol-phosphate aminotransferase
B: histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,91022
Polymers81,5082
Non-polymers1,40120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-149 kcal/mol
Surface area27030 Å2
MethodPISA
2
C: histidinol-phosphate aminotransferase
D: histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,26026
Polymers81,5082
Non-polymers1,75124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12030 Å2
ΔGint-187 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.039, 93.082, 110.518
Angle α, β, γ (deg.)90.000, 106.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
histidinol-phosphate aminotransferase


Mass: 40754.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 25495946, MTR_6g033540
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A072U7F9, histidinol-phosphate transaminase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / 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.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1598 / 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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium acetate; 0.1M BIS_TRIS pH6.5; 25% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→56.43 Å / Num. obs: 252775 / % possible obs: 99.6 % / Redundancy: 6.765 % / Biso Wilson estimate: 18.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.086 / Χ2: 0.82 / Net I/σ(I): 13.71 / Num. measured all: 1710052
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
1.45-1.546.5851.3591.326676540929405080.6281.47599
1.54-1.646.7820.8432.2926007138484383470.8290.91399.6
1.64-1.786.8110.5283.924304435806356830.9310.57199.7
1.78-1.956.6850.2967.2521972833021328700.9770.32199.5
1.95-2.176.9610.1613.3420757929846298200.9940.17399.9
2.17-2.516.7070.09121.0217666326362263400.9970.09999.9
2.51-3.0870.05931.2815636122355223380.9980.06499.9
3.08-4.356.6690.03645.3911525517297172810.9990.03999.9
4.35-56.436.7360.02853.4664586964195880.9990.03199.5

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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: 1.45→56.43 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1808 2527 1 %
Rwork0.1479 250136 -
obs0.1482 252663 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.63 Å2 / Biso mean: 26.5822 Å2 / Biso min: 8.5 Å2
Refinement stepCycle: final / Resolution: 1.45→56.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11385 0 186 1630 13201
Biso mean--50.64 40.83 -
Num. residues----1441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.480.31651370.2768136181375598
1.48-1.510.29071400.25011382413964100
1.51-1.540.26161400.22611385113991100
1.54-1.580.30671400.21181385013990100
1.58-1.620.21961400.19971383613976100
1.62-1.660.26931400.19521387614016100
1.66-1.710.23191400.17811381913959100
1.71-1.760.221400.15731390214042100
1.76-1.830.19171400.1477138531399399
1.83-1.90.2171400.14061389714037100
1.9-1.990.15351410.13871386814009100
1.99-2.090.15591400.13561389614036100
2.09-2.220.15371410.12761398314124100
2.22-2.390.17521410.12731395314094100
2.39-2.630.16551420.13381398814130100
2.63-3.020.16881400.13591395514095100
3.02-3.80.17141410.13641403814179100
3.8-56.430.15931440.1474141291427399

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