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- PDB-6fu7: ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter a... -

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Basic information

Entry
Database: PDB / ID: 6fu7
TitleATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter arcticus in complex with PRATP
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
PHOSPHORIBOSYL ATP / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase regulatory subunit
Similarity search - Component
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 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 1.1Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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)138,43111
Polymers136,7404
Non-polymers1,6917
Water2,684149
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)276,86322
Polymers273,4808
Non-polymers3,38314
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Buried area29930 Å2
ΔGint-216 kcal/mol
Surface area100100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.820, 146.780, 94.460
Angle α, β, γ (deg.)90.000, 101.770, 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
12LEULEUSERSERCC22 - 22623 - 227
22LEULEUSERSERDD22 - 22623 - 227

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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Non-polymers , 5 types, 156 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PRT / PHOSPHORIBOSYL ATP / [[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanylidene-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 719.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H25N5O20P4
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
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: 2.31→73.39 Å / Num. obs: 58950 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 54.3 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.045 / Rrim(I) all: 0.086 / Net I/σ(I): 10.4
Reflection shellResolution: 2.31→2.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.835 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4414 / CC1/2: 0.541 / Rpim(I) all: 0.494 / Rrim(I) all: 0.973 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5m8h


Resolution: 2.31→73.39 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 18.598 / SU ML: 0.212 / SU R Cruickshank DPI: 0.3526 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.353 / ESU R Free: 0.233
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 2916 4.9 %RANDOM
Rwork0.2118 ---
obs0.2134 56018 99.14 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 212.99 Å2 / Biso mean: 78.717 Å2 / Biso min: 32.23 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å20.77 Å2
2--0.68 Å20 Å2
3----3.44 Å2
Refinement stepCycle: final / Resolution: 2.31→73.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9073 0 100 149 9322
Biso mean--90.78 57.77 -
Num. residues----1167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199339
X-RAY DIFFRACTIONr_bond_other_d0.0020.028818
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.98512689
X-RAY DIFFRACTIONr_angle_other_deg0.9253.00220405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97751165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23224.153419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.705151603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.931566
X-RAY DIFFRACTIONr_chiral_restr0.0730.21496
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210294
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021812
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A226320.08
12B226320.08
21C116440.1
22D116440.1
LS refinement shellResolution: 2.31→2.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 233 -
Rwork0.315 4180 -
all-4413 -
obs--99.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.98320.20750.03221.2943-0.11232.8412-0.1250.2074-0.2347-0.260.06130.050.8444-0.140.06370.3645-0.10840.03690.0768-0.0180.3405-73.267-10.96513.966
21.07380.50570.1991.08450.27331.5249-0.01740.0480.03930.0511-0.0209-0.0773-0.0820.26380.03830.0493-0.03260.01580.05740.02480.2751-59.76511.41427.027
31.9145-0.6619-1.52152.08390.27533.5221-0.0045-0.4601-0.15030.1048-0.1094-0.0170.55290.65810.11380.47550.2261-0.01740.46470.1090.3914-20.805-13.62821.985
41.5145-0.2085-1.41421.47450.48024.0755-0.0148-0.23160.14820.12450.0533-0.14730.03410.6615-0.03860.12010.0073-0.0270.4707-0.0460.4476-22.92411.29626.473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 387
2X-RAY DIFFRACTION2B1 - 387
3X-RAY DIFFRACTION3C22 - 227
4X-RAY DIFFRACTION4D21 - 227

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