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- PDB-6fd9: Catalytic subunit HisG from Psychrobacter arcticus ATP phosphorib... -

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Basic information

Entry
Database: PDB / ID: 6fd9
TitleCatalytic subunit HisG from Psychrobacter arcticus ATP phosphoribosyltransferase (HisZG ATPPRT) in complex with AMP
ComponentsATP phosphoribosyltransferase
KeywordsTRANSFERASE / phosphoribosyltransferase / HisG / catalytic / cold-adapted
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. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsAlphey, M.S. / Ge, Y. / Fisher, G. / Czekster, C.M. / Naismith, J.H. / da Silva, R.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M010996/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2018
Title: Catalytic and Anticatalytic Snapshots of a Short-Form ATP Phosphoribosyltransferase
Authors: Alphey, M.S. / Fisher, G. / Hirschi, J.S. / Stroek, R. / Ge, Y. / Gould, E.R. / Czekster, C.M. / Liu, H. / Florence, G.J. / Vetticatt, M.J. / Naismith, J.H. / da Silva, R.G.
History
DepositionDec 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5882
Polymers25,2411
Non-polymers3471
Water1,54986
1
A: ATP phosphoribosyltransferase
hetero molecules

A: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1764
Polymers50,4822
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3510 Å2
ΔGint-26 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.820, 33.940, 92.407
Angle α, β, γ (deg.)90.000, 105.360, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-646-

HOH

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Components

#1: Protein ATP phosphoribosyltransferase / ATP-PRTase


Mass: 25240.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues from N- and C-termini are missing from coordinate sequence due to flexibility - electron density missing. Initial glycine remains after affinity-tag cleavage.
Source: (gene. exp.) Psychrobacter arcticus (strain DSM 17307 / 273-4) (bacteria)
Strain: DSM 17307 / 273-4 / Gene: hisG, Psyc_1903 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C43 / References: UniProt: Q4FQF7, ATP phosphoribosyltransferase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
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 pH6.5, 0.1M K/Na tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 6, 2017 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→26.61 Å / Num. obs: 10299 / % possible obs: 93 % / Redundancy: 3.6 % / CC1/2: 0.981 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.105 / Rrim(I) all: 0.199 / Net I/σ(I): 5.8 / Num. measured all: 37047 / Scaling rejects: 9
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.549 / Num. unique obs: 827 / CC1/2: 0.706 / Rpim(I) all: 0.336 / Rrim(I) all: 0.645 / % possible all: 87.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.32data scaling
MOLREPphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M8H chain E

5m8h


Resolution: 2.2→26.61 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.367 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.325 / ESU R Free: 0.223
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 510 5 %RANDOM
Rwork0.185 ---
obs0.1874 9789 93.23 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 64.29 Å2 / Biso mean: 25.922 Å2 / Biso min: 14.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å20.09 Å2
2---0.93 Å20 Å2
3---2.17 Å2
Refinement stepCycle: final / Resolution: 2.2→26.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 23 86 1716
Biso mean--42.72 30.25 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191656
X-RAY DIFFRACTIONr_bond_other_d0.0020.021614
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9882249
X-RAY DIFFRACTIONr_angle_other_deg0.92.9923729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7815208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36723.82468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07815289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4291513
X-RAY DIFFRACTIONr_chiral_restr0.0710.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211817
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02315
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 34 -
Rwork0.262 676 -
all-710 -
obs--88.2 %

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