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

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Basic information

Entry
Database: PDB / ID: 6fcc
TitleCatalytic subunit HisG from Psychrobacter arcticus ATP phosphoribosyltransferase (HisZG ATPPRT)
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
L(+)-TARTARIC ACID / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 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 20, 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)25,3912
Polymers25,2411
Non-polymers1501
Water2,648147
1
A: ATP phosphoribosyltransferase
hetero molecules

A: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7824
Polymers50,4822
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2950 Å2
ΔGint-12 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.980, 33.870, 92.367
Angle α, β, γ (deg.)90.000, 105.920, 90.000
Int Tables number5
Space group name H-MI121

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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: N- and C-terminal residues were disordered so do not appear in the coordinate sequence. The initial G remains after TEV-cleavage of affinity tag.
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) / Variant (production host): C43 / References: UniProt: Q4FQF7, ATP phosphoribosyltransferase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 41.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 10mg/ml-1 protein (buffer 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: Oct 24, 2017 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→21.5 Å / Num. obs: 17009 / % possible obs: 98.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 12.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.1 / Rrim(I) all: 0.16 / Net I/σ(I): 6.9
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 861 / CC1/2: 0.86 / Rpim(I) all: 0.38 / Rrim(I) all: 0.6 / % possible all: 79.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5m8h


Resolution: 1.89→21.5 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.258 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.157
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 821 4.8 %RANDOM
Rwork0.2067 ---
obs0.2086 16188 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 60.15 Å2 / Biso mean: 17.558 Å2 / Biso min: 1.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20.21 Å2
2---1.28 Å20 Å2
3---1.24 Å2
Refinement stepCycle: final / Resolution: 1.89→21.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 10 147 1764
Biso mean--34.59 27.28 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191658
X-RAY DIFFRACTIONr_bond_other_d0.0020.021630
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.9992253
X-RAY DIFFRACTIONr_angle_other_deg0.89333768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1245214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12923.82468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97815293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1821513
X-RAY DIFFRACTIONr_chiral_restr0.070.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211836
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02317
LS refinement shellResolution: 1.886→1.935 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 43 -
Rwork0.318 949 -
all-992 -
obs--79.74 %

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