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- PDB-6fua: ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter a... -

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Basic information

Entry
Database: PDB / ID: 6fua
TitleATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter arcticus in complex with PRPP and ADP
Components
  • ATP phosphoribosyltransferase
  • ATP phosphoribosyltransferase regulatory subunit
KeywordsTRANSFERASE / ATP phosphoribosyltransferase / HisZG / cold-adapted
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / L-histidine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
ATP phosphoribosyltransferase regulatory subunit / ATP phosphoribosyltransferase HisG, short form / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase ...ATP phosphoribosyltransferase regulatory subunit / ATP phosphoribosyltransferase HisG, short form / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-PRP / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase regulatory subunit
Similarity search - Component
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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
DepositionFeb 26, 2018Deposition 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP phosphoribosyltransferase regulatory subunit
B: ATP phosphoribosyltransferase regulatory subunit
C: ATP phosphoribosyltransferase
D: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,50512
Polymers136,7404
Non-polymers1,7658
Water37821
1
A: ATP phosphoribosyltransferase regulatory subunit
B: ATP phosphoribosyltransferase regulatory subunit
C: ATP phosphoribosyltransferase
D: ATP phosphoribosyltransferase
hetero molecules

A: ATP phosphoribosyltransferase regulatory subunit
B: ATP phosphoribosyltransferase regulatory subunit
C: ATP phosphoribosyltransferase
D: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,01024
Polymers273,4808
Non-polymers3,53016
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)101.570, 146.240, 93.800
Angle α, β, γ (deg.)90.000, 102.980, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVALAA1 - 3872 - 388
21METMETVALVALBB1 - 3872 - 388
12PHEPHEILEILECC21 - 22722 - 228
22PHEPHEILEILEDD21 - 22722 - 228

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein ATP phosphoribosyltransferase regulatory subunit


Mass: 43129.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Missing sections are due to flexible regions not visible in the electron density maps. N-terminal Gly remains after tag cleavage.
Source: (gene. exp.) Psychrobacter arcticus (strain DSM 17307 / 273-4) (bacteria)
Strain: DSM 17307 / 273-4 / Gene: hisZ, Psyc_0676 / Plasmid: pJexpress414 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4FTX3
#2: Protein ATP phosphoribosyltransferase / ATP-PRTase


Mass: 25240.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Missing sections are due to flexible regions not visible in the electron density maps. N-terminal Gly remains after tag cleavage.
Source: (gene. exp.) Psychrobacter arcticus (strain DSM 17307 / 273-4) (bacteria)
Strain: DSM 17307 / 273-4 / Gene: hisG, Psyc_1903 / Plasmid: pJexpress431 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43(DE3) / References: UniProt: Q4FQF7, ATP phosphoribosyltransferase

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Sugars , 1 types, 2 molecules

#5: 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.: 2 / Source method: obtained synthetically / Formula: C5H13O14P3 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 27 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8mg mL-1 protein (in 20mM Tris pH7, 50mM KCl, 10mM MgCl2, 2mM DTT, 0.5mM histidine) mixed in 1:1 ratio with precipitant solution (11% PEG3350, 100mM bicine pH8.5, 150mM SrCl2, 150mM KBr, 2% 1,6-hexanediol)

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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: Mar 3, 2017 / Details: Varimax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→35.04 Å / Num. obs: 32533 / % possible obs: 99.1 % / Redundancy: 3.7 % / CC1/2: 0.986 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.115 / Rrim(I) all: 0.224 / Net I/σ(I): 6.4 / Num. measured all: 120442 / Scaling rejects: 46
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.707 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4710 / CC1/2: 0.581 / Rpim(I) all: 1.032 / Rrim(I) all: 1.998 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.31data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M8H partial model

5m8h


Resolution: 2.8→35.04 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.876 / SU B: 26.197 / SU ML: 0.445 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.439
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 1623 5 %RANDOM
Rwork0.246 ---
obs0.2478 30909 98.98 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 138.05 Å2 / Biso mean: 65.218 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-3.59 Å20 Å21.19 Å2
2--0.2 Å20 Å2
3----3.92 Å2
Refinement stepCycle: final / Resolution: 2.8→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9022 0 102 21 9145
Biso mean--87.4 37.87 -
Num. residues----1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199276
X-RAY DIFFRACTIONr_bond_other_d0.0020.028737
X-RAY DIFFRACTIONr_angle_refined_deg1.321.97512597
X-RAY DIFFRACTIONr_angle_other_deg0.9342.99720212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88251152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38424.197417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.708151585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0671564
X-RAY DIFFRACTIONr_chiral_restr0.0680.21479
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210219
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021799
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A222680.1
12B222680.1
21C117180.11
22D117180.11
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 132 -
Rwork0.412 2256 -
all-2388 -
obs--98.27 %

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