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- PDB-6czl: Crystal structure of Medicago truncatula ATP-phosphoribosyltransf... -

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Basic information

Entry
Database: PDB / ID: 6czl
TitleCrystal structure of Medicago truncatula ATP-phosphoribosyltransferase in relaxed form
ComponentsATP phosphoribosyltransferase catalytic subunit
KeywordsTRANSFERASE / ATP-PRT / PRPP / allosteric regulation / histidine biosynthesis
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / nucleotide binding / magnesium ion binding / cytoplasm
Similarity search - Function
Histidine biosynthesis HisG, C-terminal / HisG, C-terminal domain / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal
Similarity search - Domain/homology
ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.92 Å
AuthorsRuszkowski, M.
CitationJournal: Biochem. J. / Year: 2018
Title: Guarding the gateway to histidine biosynthesis in plants:Medicago truncatulaATP-phosphoribosyltransferase in relaxed and tense states.
Authors: Ruszkowski, M.
History
DepositionApr 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP phosphoribosyltransferase catalytic subunit
B: ATP phosphoribosyltransferase catalytic subunit
C: ATP phosphoribosyltransferase catalytic subunit
D: ATP phosphoribosyltransferase catalytic subunit
E: ATP phosphoribosyltransferase catalytic subunit
F: ATP phosphoribosyltransferase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,11217
Polymers231,4396
Non-polymers67311
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22960 Å2
ΔGint-142 kcal/mol
Surface area87550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.826, 195.621, 100.209
Angle α, β, γ (deg.)90.00, 95.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ATP phosphoribosyltransferase catalytic subunit


Mass: 38573.184 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11438625, MTR_4g130680
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G7JFL4
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 4.21 Å3/Da / Density % sol: 70.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 2.63 M NaCl, 100 mM Bis-Tris propane pH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.978 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 9, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.92→50 Å / Num. obs: 82460 / % possible obs: 99.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.076 / Net I/σ(I): 15.2
Reflection shellResolution: 2.92→3.09 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 12719 / Rrim(I) all: 1.05 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.92→39.17 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 37.306 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R: 0.524 / ESU R Free: 0.321 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1237 1.5 %RANDOM
Rwork0.197 ---
obs0.198 81223 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 100.861 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20.16 Å2
2---0.98 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.92→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15480 0 36 40 15556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01915745
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215600
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.96321277
X-RAY DIFFRACTIONr_angle_other_deg0.914335926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0752000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25324.4650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.676152864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.99515110
X-RAY DIFFRACTIONr_chiral_restr0.0720.22467
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02117646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023328
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.076.368036
X-RAY DIFFRACTIONr_mcbond_other2.076.368035
X-RAY DIFFRACTIONr_mcangle_it3.7319.53110024
X-RAY DIFFRACTIONr_mcangle_other3.739.53110025
X-RAY DIFFRACTIONr_scbond_it1.7616.67709
X-RAY DIFFRACTIONr_scbond_other1.7616.67709
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2419.78811254
X-RAY DIFFRACTIONr_long_range_B_refined5.86848.59916310
X-RAY DIFFRACTIONr_long_range_B_other5.86748.60316311
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.916→2.991 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 82 -
Rwork0.361 5377 -
obs--89.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.75830.3158-0.48191.3766-0.81611.9530.1015-0.21990.28130.09170.0811-0.1977-0.19170.2367-0.18260.1036-0.13350.14460.3553-0.14060.492534.345113.92210.672
21.12250.2152-0.8220.52490.00040.847-0.13340.09140.104-0.3529-0.00030.0090.0068-0.06060.13370.47070.01680.09790.10120.15840.45775.1123.685-12.772
31.40160.7763-0.45671.84760.00850.8240.06580.103-0.0983-0.2905-0.0159-0.25570.07430.1013-0.050.37670.01710.18170.357-0.00210.129526.15791.384-20.111
40.9070.3965-0.33832.0865-0.96761.4048-0.0308-0.12550.22710.2383-0.13180.2576-0.0338-0.16670.16260.1109-0.03750.16550.3256-0.12350.4163-18.379104.13620.937
52.37651.1889-0.13091.573-0.02840.613-0.0201-0.1723-0.20950.2336-0.0705-0.1780.30470.14340.09050.48030.02410.11830.33290.08790.085910.64180.9831.427
60.8630.0759-0.47630.7782-0.23520.95060.03160.2049-0.0516-0.1009-0.04660.27980.3472-0.09080.0150.3921-0.12470.10880.2001-0.04350.3336-10.28472.765-0.618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 373
2X-RAY DIFFRACTION2B36 - 373
3X-RAY DIFFRACTION3C36 - 373
4X-RAY DIFFRACTION4D36 - 373
5X-RAY DIFFRACTION5E36 - 373
6X-RAY DIFFRACTION6F36 - 373

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