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- PDB-7z6r: Psychrobacter arcticus ATPPRT (HisGZ) R56A mutant bound to ATP an... -

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Basic information

Entry
Database: PDB / ID: 7z6r
TitlePsychrobacter arcticus ATPPRT (HisGZ) R56A mutant bound to ATP and PRPP
Components
  • ATP phosphoribosyltransferase regulatory subunit
  • ATP phosphoribosyltransferase
KeywordsTRANSFERASE / phosphoribosyltransferase / ATPPRT / PRPP / HisGZ / histidine / biosynthesis / allosteric
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / 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 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
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: 2.55 Å
AuthorsAlphey, M.S. / Fisher, G. / da Silva, R.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M010996/1 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation.
Authors: Fisher, G. / Corbella, M. / Alphey, M.S. / Nicholson, J. / Read, B.J. / Kamerlin, S.C.L. / da Silva, R.G.
History
DepositionMar 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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)138,3628
Polymers136,5684
Non-polymers1,7954
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-71 kcal/mol
Surface area49470 Å2
Unit cell
Length a, b, c (Å)102.155, 145.525, 93.812
Angle α, β, γ (deg.)90.000, 102.480, 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: 0 / Refine code: 0

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

#1: Protein ATP phosphoribosyltransferase regulatory subunit


Mass: 43129.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter arcticus (bacteria) / Gene: hisZ, Psyc_0676 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4FTX3
#2: Protein ATP phosphoribosyltransferase / / ATP-PRT / ATP-PRTase


Mass: 25154.850 Da / Num. of mol.: 2 / Mutation: R56A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter arcticus (bacteria) / Strain: DSM 17307 / VKM B-2377 / 273-4 / Gene: hisG, Psyc_1903 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q4FQF7, ATP phosphoribosyltransferase
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#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 / Phosphoribosyl pyrophosphate


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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 50.44 %
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 (12% PEG3350, 100mM bicine pH8.5, 150mM SrCl2, 150mM KBr, 2% 1,6-hexanediol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.55→56.97 Å / Num. obs: 43754 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 53.1 Å2 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.073 / Rrim(I) all: 0.187 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
2.55-2.597.13.1750.821211.2743.42499.3
6.91-56.9960.04843.922490.0210.053100

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.523
Highest resolutionLowest resolution
Rotation56.97 Å3.04 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia23.4.2data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FU2

6fu2


Resolution: 2.55→56.97 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2508 / WRfactor Rwork: 0.2098 / FOM work R set: 0.6855 / SU B: 39.307 / SU ML: 0.359 / SU R Cruickshank DPI: 0.645 / SU Rfree: 0.3229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.645 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 2156 4.9 %RANDOM
Rwork0.233 ---
obs0.2351 41555 99.82 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 144.86 Å2 / Biso mean: 68.237 Å2 / Biso min: 36.89 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å20 Å2-0.6 Å2
2--2.98 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 2.55→56.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8394 0 106 16 8516
Biso mean--105.47 58.35 -
Num. residues----1157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138661
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177881
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.63711787
X-RAY DIFFRACTIONr_angle_other_deg1.2081.57318079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79751148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24321.958383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.801151274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8151549
X-RAY DIFFRACTIONr_chiral_restr0.0520.21149
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029879
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021770
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A97920.1
12B97920.1
21C54610.07
22D54610.07
LS refinement shellResolution: 2.55→2.611 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.425 138 -
Rwork0.394 3051 -
obs--99.25 %
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)
10.26860.35690.21660.56770.04361.2696-0.09520.10840.0138-0.09570.14040.07440.395-0.0296-0.04520.645-0.11420.15420.07450.00390.0797-22.437-9.93115.006
20.43730.3304-0.0010.44530.10060.8676-0.04820.06130.06030.01330.03920.0358-0.020.15260.0090.4458-0.03980.14290.06730.02850.087-9.29811.72926.992
31.0446-0.6607-0.73041.22470.15960.7075-0.0003-0.0592-0.06460.1015-0.11190.04430.20820.16070.11220.70490.17140.17760.1630.03780.051529.804-13.87421.968
40.8491-0.3365-0.83821.22270.5122.96550.055-0.1860.11680.02580.0869-0.2809-0.02640.4112-0.1420.38320.02970.11910.2143-0.08630.236127.58611.66326.242
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 387
2X-RAY DIFFRACTION2B1 - 387
3X-RAY DIFFRACTION3C21 - 227
4X-RAY DIFFRACTION4D21 - 228

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