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

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Basic information

Entry
Database: PDB / ID: 6czm
TitleCrystal structure of Medicago truncatula ATP-phosphoribosyltransferase in tense 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
ADENOSINE MONOPHOSPHATE / HISTIDINE / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)234,45918
Polymers231,4396
Non-polymers3,02012
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22810 Å2
ΔGint-108 kcal/mol
Surface area87140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.170, 178.660, 92.110
Angle α, β, γ (deg.)90.00, 105.71, 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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: histidine and AMP (5 mM each) were added to the protein solution supplemented with 10 mM MgCl2 and 100 mM KCl and incubated for 1 h. Reservoir solution: 2.53 M NaCl, 100 mM Bis-Tris propane ...Details: histidine and AMP (5 mM each) were added to the protein solution supplemented with 10 mM MgCl2 and 100 mM KCl and incubated for 1 h. Reservoir solution: 2.53 M NaCl, 100 mM Bis-Tris propane pH 6.3 and 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 62118 / % possible obs: 99.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.055 / Net I/σ(I): 18.4
Reflection shellResolution: 2.88→2.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4580 / Rrim(I) all: 0.93 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Domains of MedtrATP-PRT1 in relaxed form

Resolution: 2.88→43.295 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.83
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1055 1.7 %Random
Rwork0.191 ---
obs0.192 62109 99.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.88→43.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15156 0 204 20 15380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715596
X-RAY DIFFRACTIONf_angle_d1.03321087
X-RAY DIFFRACTIONf_dihedral_angle_d16.0969456
X-RAY DIFFRACTIONf_chiral_restr0.0582444
X-RAY DIFFRACTIONf_plane_restr0.0072694
LS refinement shellResolution: 2.88→3.01 Å
RfactorNum. reflection% reflection
Rfree0.344 132 -
Rwork0.307 7553 -
obs--99 %
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)
11.3085-0.26550.18031.2581-0.7792.88450.07820.085-0.1280.15890.06510.06690.0266-0.1431-0.10590.55710.04120.05370.3947-0.02110.5222-17.4509106.1127-5.3228
22.4723-1.0968-0.05254.42340.22060.9921-0.0357-0.208-0.63940.56870.0356-0.09980.27020.12530.09410.9001-0.0484-0.18030.7457-0.02350.6138-10.515681.3828-27.8576
32.40490.5049-0.0581.60.42832.16780.04260.0069-0.1083-0.1060.0284-0.3411-0.27820.5173-0.08830.7383-0.07250.08560.7360.05340.47869.3301109.7635-27.3094
41.07320.44970.41682.4834-0.0621.0361-0.0591-0.1001-0.0304-0.29270.08810.3676-0.02540.0575-0.07830.79740.00650.0740.4464-0.04780.74359.40665.331517.3397
51.5843-0.34750.05232.1787-0.71561.4750.13540.1520.08510.1199-0.13780.1964-0.3801-0.1202-0.09140.6753-0.0095-0.0710.6497-0.16420.460422.07996.605323.9427
61.93730.1494-0.49041.963-0.04554.26640.12231.3325-0.114-0.5321-0.2518-0.1648-0.5395-0.48570.01730.74440.2798-0.02221.4567-0.03250.742138.262477.41920.959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 36:373 OR RESID 401:402 ) )A36 - 373
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 36:373 OR RESID 401:402 ) )A401 - 402
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 39:372 OR RESID 401:402 ) )B39 - 372
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 39:372 OR RESID 401:402 ) )B401 - 402
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 33:372 OR RESID 401:402 ) )C33 - 372
6X-RAY DIFFRACTION3( CHAIN C AND ( RESID 33:372 OR RESID 401:402 ) )C401 - 402
7X-RAY DIFFRACTION4( CHAIN D AND ( RESID 36:373 OR RESID 401:402 ) )D36 - 373
8X-RAY DIFFRACTION4( CHAIN D AND ( RESID 36:373 OR RESID 401:402 ) )D401 - 402
9X-RAY DIFFRACTION5( CHAIN E AND ( RESID 31:372 OR RESID 401:402 ) )E31 - 372
10X-RAY DIFFRACTION5( CHAIN E AND ( RESID 31:372 OR RESID 401:402 ) )E401 - 402
11X-RAY DIFFRACTION6( CHAIN F AND ( RESID 38:372 OR RESID 401:402 ) )F38 - 372
12X-RAY DIFFRACTION6( CHAIN F AND ( RESID 38:372 OR RESID 401:402 ) )F401 - 402

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