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- PDB-5ubi: Catalytic core domain of Adenosine triphosphate phosphoribosyltra... -

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Basic information

Entry
Database: PDB / ID: 5ubi
TitleCatalytic core domain of Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni with bound PRPP
ComponentsATP phosphoribosyltransferase
KeywordsTRANSFERASE / Histidine-biosynthesis / HisG / PRPP
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
ATP phosphoribosyltransferase HisG, long form / Histidine biosynthesis HisG, C-terminal / HisG, C-terminal domain / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal ...ATP phosphoribosyltransferase HisG, long form / Histidine biosynthesis HisG, C-terminal / HisG, C-terminal domain / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-PRP / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsMittelstaedt, G. / Jiao, W. / Livingstone, E.K. / Parker, E.J.
Citation
Journal: Biochem. J. / Year: 2018
Title: A dimeric catalytic core relates the short and long forms of ATP-phosphoribosyltransferase.
Authors: Mittelstadt, G. / Jiao, W. / Livingstone, E.K. / Moggre, G.J. / Nazmi, A.R. / Parker, E.J.
#1: Journal: Protein Sci. / Year: 2016
Title: Campylobacter jejuni adenosine triphosphate phosphoribosyltransferase is an active hexamer that is allosterically controlled by the twisting of a regulatory tail.
Authors: Mittelstaedt, G. / Moggre, G.J. / Panjikar, S. / Nazmi, A.R. / Parker, E.J.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Jul 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: 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
B: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,20317
Polymers50,6812
Non-polymers1,52215
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-219 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.003, 79.690, 91.119
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 4 - 220 / Label seq-ID: 5 - 221

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe authors state that the protein exists as dimer of 50 kDa in solution as evidenced by SEC, AUC, and light scattering experiments

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein ATP phosphoribosyltransferase / ATP-PRTase


Mass: 25340.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (strain RM1221) (Campylobacter)
Strain: RM1221 / Gene: hisG, CJE1769 / Plasmid: pDEST15 / Details (production host): N-terminal GST tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*(DE3) / References: UniProt: Q5HSJ4, ATP phosphoribosyltransferase
#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 , 5 types, 220 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.37 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate pH 5.0, 0.01 M ZnCl2, 7-10% PEG 6000 formed crystals were soaked with 3 mM PRPP for 30-60 min
PH range: 5 / Temp details: temperature controlled

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.959 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.959 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28897 / % possible obs: 99.9 % / Redundancy: 14.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Net I/σ(I): 27.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.7 / CC1/2: 0.896 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: single chain of 5UB9

5ub9


Resolution: 2.14→45.56 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.324 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28334 1371 5 %RANDOM
Rwork0.20931 ---
obs0.2131 25799 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.047 Å2
Baniso -1Baniso -2Baniso -3
1--17.1 Å2-0 Å20 Å2
2--3.62 Å20 Å2
3---13.48 Å2
Refinement stepCycle: 1 / Resolution: 2.14→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3351 0 72 207 3630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193509
X-RAY DIFFRACTIONr_bond_other_d0.0040.023417
X-RAY DIFFRACTIONr_angle_refined_deg1.5042.0094751
X-RAY DIFFRACTIONr_angle_other_deg0.98337850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7525450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31425.067150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52315634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9051523
X-RAY DIFFRACTIONr_chiral_restr0.0820.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023969
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02736
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7842.4661791
X-RAY DIFFRACTIONr_mcbond_other3.7142.461787
X-RAY DIFFRACTIONr_mcangle_it4.3323.6812242
X-RAY DIFFRACTIONr_mcangle_other4.3323.6822243
X-RAY DIFFRACTIONr_scbond_it4.4952.7871718
X-RAY DIFFRACTIONr_scbond_other4.4922.7871718
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2324.0822510
X-RAY DIFFRACTIONr_long_range_B_refined5.44820.3333992
X-RAY DIFFRACTIONr_long_range_B_other5.44920.3383993
X-RAY DIFFRACTIONr_rigid_bond_restr3.78736926
X-RAY DIFFRACTIONr_sphericity_free33.13566
X-RAY DIFFRACTIONr_sphericity_bonded17.78157036
Refine LS restraints NCS

Ens-ID: 1 / Number: 12410 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 109 -
Rwork0.367 1878 -
obs--99.75 %
Refinement TLS params.

S22: -0.0064 Å ° / 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 °)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)
10.2357-0.0809-0.01960.3010.01870.03420.02020.0340.004-0.07450.0182-0.0164-0.0139-0.01370.2170.0043-0.01250.0330.00270.0083-15.1672-15.1916.5079
20.15320.0614-0.04080.2677-0.0170.2346-0.0067-0.0125-0.0366-0.0047-0.0390.0136-0.00610.0130.19080.00160.00180.01370.01670.02661.2326-12.279935.5662
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 221
2X-RAY DIFFRACTION2B4 - 225

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