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- PDB-6fu2: ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter a... -

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Basic information

Entry
Database: PDB / ID: 6fu2
TitleATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter arcticus in complex with PRPP and ATP
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'-TRIPHOSPHATE / Chem-PRP / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase regulatory subunit
Similarity search - Component
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.71 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
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)138,95013
Polymers136,7404
Non-polymers2,2109
Water1629
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)277,89926
Polymers273,4808
Non-polymers4,41918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area36140 Å2
ΔGint-200 kcal/mol
Surface area95120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.720, 146.200, 94.510
Angle α, β, γ (deg.)90.000, 102.160, 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 (bacteria) / Gene: hisZ, Psyc_0676 / Plasmid: pJexpress414 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 (bacteria) / Gene: hisG, Psyc_1903 / Plasmid: pJexpress431 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q4FQF7, ATP phosphoribosyltransferase

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Sugars , 1 types, 2 molecules

#4: 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
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 16 molecules

#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
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: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.71→73.11 Å / Num. obs: 36859 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 64.8 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.052 / Rrim(I) all: 0.107 / Net I/σ(I): 10.8
Reflection shellResolution: 2.71→2.78 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.095 / Num. unique obs: 2720 / CC1/2: 0.581 / Rpim(I) all: 0.59 / Rrim(I) all: 1.248 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5m8h


Resolution: 2.71→39.05 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 16.129 / SU ML: 0.302 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.344
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 1825 5 %RANDOM
Rwork0.2008 ---
obs0.2028 35007 99.5 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 171.71 Å2 / Biso mean: 80.589 Å2 / Biso min: 47.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å23.02 Å2
2---0.74 Å20 Å2
3----1.83 Å2
Refinement stepCycle: final / Resolution: 2.71→39.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9097 0 132 9 9238
Biso mean--89.46 64.24 -
Num. residues----1169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0199384
X-RAY DIFFRACTIONr_bond_other_d0.0020.028836
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.97812749
X-RAY DIFFRACTIONr_angle_other_deg0.8872.99720443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05451163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7724.184423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.562151602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0231566
X-RAY DIFFRACTIONr_chiral_restr0.0660.21494
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210323
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021817
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A22648
12B22648
21C12230
22D12230
LS refinement shellResolution: 2.71→2.78 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 137 -
Rwork0.35 2565 -
all-2702 -
obs--99.63 %

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