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- PDB-7z8u: Catalytic subunit HisG R56A mutant from Psychrobacter arcticus AT... -

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Basic information

Entry
Database: PDB / ID: 7z8u
TitleCatalytic subunit HisG R56A mutant from Psychrobacter arcticus ATPPRT (HisGZ) in complex with ATP and PRPP
ComponentsATP phosphoribosyltransferase
KeywordsTRANSFERASE / ATP / phosphoribosyltransferase / ATPPRT / PRPP / HisG / HisGZ / histidine / biosynthesis / allosteric
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
ATP phosphoribosyltransferase HisG, short form / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature.
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chem-PRP / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsAlphey, M.S. / Fisher, G. / da Silva, R.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M010996/1 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation.
Authors: Fisher, G. / Corbella, M. / Alphey, M.S. / Nicholson, J. / Read, B.J. / Kamerlin, S.C.L. / da Silva, R.G.
History
DepositionMar 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 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

Downloads & links

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Assembly

Deposited unit
A: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0764
Polymers25,1551
Non-polymers9223
Water75742
1
A: ATP phosphoribosyltransferase
hetero molecules

A: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1538
Polymers50,3102
Non-polymers1,8436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5750 Å2
ΔGint-57 kcal/mol
Surface area17800 Å2
Unit cell
Length a, b, c (Å)70.090, 33.900, 89.265
Angle α, β, γ (deg.)90.000, 103.520, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein ATP phosphoribosyltransferase / ATP-PRT / ATP-PRTase


Mass: 25154.850 Da / Num. of mol.: 1 / Mutation: R56A
Source method: isolated from a genetically manipulated source
Details: The glycine prior to the initiating methionine remains after his-tag cleavage. R56A mutation
Source: (gene. exp.) Psychrobacter arcticus (bacteria) / Strain: DSM 17307 / VKM B-2377 / 273-4 / Gene: hisG, Psyc_1903 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4FQF7, ATP phosphoribosyltransferase
#2: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H13O14P3 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.98 Å3/Da / Density % sol: 38.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10mg/ml protein in 20mM Tris HCl pH8.0, 50mM KCl, 10mM MgCl2, 2mM DTT mixed 1:1 with 32% PEG 3350, 0.1M MOPS pH6.0, 0.1M K/Na tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 20, 2019 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→22.02 Å / Num. obs: 13035 / % possible obs: 93.8 % / Redundancy: 3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.072 / Rrim(I) all: 0.13 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.052.60.36423368940.8430.2670.4532.588.2
8.94-22.013.20.0554111280.9950.0340.0651681.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.425
Highest resolutionLowest resolution
Rotation22.01 Å2.07 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.7.4data scaling
MOLREPphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FCT

6fct


Resolution: 2→22.02 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.897 / SU B: 7.539 / SU ML: 0.195 / SU R Cruickshank DPI: 0.2495 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 623 4.8 %RANDOM
Rwork0.2216 ---
obs0.2239 12411 92.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.66 Å2 / Biso mean: 19.809 Å2 / Biso min: 8.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å2-0.76 Å2
2---2.52 Å20 Å2
3---4.23 Å2
Refinement stepCycle: final / Resolution: 2→22.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 54 42 1669
Biso mean--37.18 20.24 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171581
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.6582253
X-RAY DIFFRACTIONr_angle_other_deg1.2441.5823658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9295206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52522.13375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55215279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0931511
X-RAY DIFFRACTIONr_chiral_restr0.0670.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021793
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02311
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 40 -
Rwork0.295 853 -
all-893 -
obs--87.38 %

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