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

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Basic information

Entry
Database: PDB / ID: 6fca
TitleCatalytic subunit HisG from Psychrobacter arcticus ATP phosphoribosyltransferase (HisZG ATPPRT) in complex with PRPP
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
Chem-PRP / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 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 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)25,6312
Polymers25,2411
Non-polymers3901
Water1,946108
1
A: ATP phosphoribosyltransferase
hetero molecules

A: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2624
Polymers50,4822
Non-polymers7802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area3240 Å2
ΔGint-24 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.570, 33.900, 90.769
Angle α, β, γ (deg.)90.000, 105.170, 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
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: 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
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.08 Å3/Da / Density % sol: 40.75 %
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: 1.5148 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5148 Å / Relative weight: 1
ReflectionResolution: 2.09→24.61 Å / Num. obs: 12446 / % possible obs: 99.2 % / Redundancy: 3.9 % / CC1/2: 0.984 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.094 / Rrim(I) all: 0.19 / Net I/σ(I): 5.6 / Num. measured all: 48170 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.09-2.1530.4929250.6590.3390.60292.4
8.87-24.613.70.061730.9950.0330.06995.7

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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: 2.09→24.61 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.135 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.191
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 608 4.9 %RANDOM
Rwork0.1914 ---
obs0.1935 11838 99.09 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 83.28 Å2 / Biso mean: 21.75 Å2 / Biso min: 12.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å2-0.33 Å2
2---1.57 Å20 Å2
3---2.41 Å2
Refinement stepCycle: final / Resolution: 2.09→24.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 22 108 1737
Biso mean--48.69 27.51 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191653
X-RAY DIFFRACTIONr_bond_other_d0.0020.021612
X-RAY DIFFRACTIONr_angle_refined_deg1.3582.0082246
X-RAY DIFFRACTIONr_angle_other_deg0.90433725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65523.82468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24615289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6841513
X-RAY DIFFRACTIONr_chiral_restr0.0710.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02313
LS refinement shellResolution: 2.091→2.145 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 38 -
Rwork0.262 800 -
all-838 -
obs--90.99 %

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