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- PDB-4yb5: Adenosine triphosphate phosphoribosyltransferase from Campylobact... -

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Basic information

Entry
Database: PDB / ID: 4yb5
TitleAdenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni in complex with the allosteric inhibitor histidine
ComponentsATP phosphoribosyltransferase
KeywordsTRANSFERASE / Phosphoribosyltransferase / hexamer / Histidine complex
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / 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. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta ...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. / Alpha-Beta Plaits - #120 / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / THIOCYANATE ION / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsMittelstaedt, G. / Moggre, G.-J. / Parker, E.J.
CitationJournal: 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: Mittelstadt, G. / Moggre, G.J. / Panjikar, S. / Nazmi, A.R. / Parker, E.J.
History
DepositionFeb 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.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_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
C: ATP phosphoribosyltransferase
D: ATP phosphoribosyltransferase
E: ATP phosphoribosyltransferase
F: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,40728
Polymers202,4486
Non-polymers1,96022
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering, equilibrium centrifugation, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28710 Å2
ΔGint-152 kcal/mol
Surface area66560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.137, 123.216, 95.701
Angle α, β, γ (deg.)90.00, 110.66, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 5 - 299 / Label seq-ID: 6 - 300

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
DetailsHexameric assembly in solution was confirmed by gel filtration, light scattering, analytic ultra centrifugation and SAXS experiments

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
ATP phosphoribosyltransferase / / ATP-PRTase


Mass: 33741.254 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (strain RM1221) (Campylobacter)
Strain: RM1221 / Gene: hisG, CJE1769 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HSJ4, ATP phosphoribosyltransferase

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Non-polymers , 6 types, 150 molecules

#2: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H10N3O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Potassium Thiocyanate, BTP, PEG3350, histidine / Temp details: temperature controlled incubator

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.959 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.959 Å / Relative weight: 1
ReflectionResolution: 2.24→48.04 Å / Num. obs: 94235 / % possible obs: 99 % / Redundancy: 5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 2
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H3D

1h3d


Resolution: 2.24→48.04 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.843 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23907 4730 5 %RANDOM
Rwork0.20883 ---
obs0.21035 89475 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.288 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å21.81 Å2
2---1.67 Å20 Å2
3---1.23 Å2
Refinement stepCycle: 1 / Resolution: 2.24→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13195 0 119 128 13442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01913471
X-RAY DIFFRACTIONr_bond_other_d0.0060.0213363
X-RAY DIFFRACTIONr_angle_refined_deg1.477218204
X-RAY DIFFRACTIONr_angle_other_deg1.264330636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85851743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88324.756513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.983152422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3871579
X-RAY DIFFRACTIONr_chiral_restr0.0750.22204
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115040
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022749
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_it3.4944.6827031
X-RAY DIFFRACTIONr_mcbond_other3.4944.6827030
X-RAY DIFFRACTIONr_mcangle_it5.0637.0138747
X-RAY DIFFRACTIONr_mcangle_other5.0627.0138748
X-RAY DIFFRACTIONr_scbond_it4.8255.2086440
X-RAY DIFFRACTIONr_scbond_other4.8255.2086440
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4387.5649458
X-RAY DIFFRACTIONr_long_range_B_refined9.36136.39814216
X-RAY DIFFRACTIONr_long_range_B_other9.3636.39814217
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A168200.08
12B168200.08
21A166260.08
22C166260.08
31A169380.08
32D169380.08
41A165580.08
42E165580.08
51A165110.09
52F165110.09
61B169080.08
62C169080.08
71B168970.09
72D168970.09
81B167390.08
82E167390.08
91B168230.08
92F168230.08
101C167010.09
102D167010.09
111C164750.09
112E164750.09
121C166740.09
122F166740.09
131D167260.08
132E167260.08
141D166610.09
142F166610.09
151E167930.08
152F167930.08
LS refinement shellResolution: 2.238→2.296 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 317 -
Rwork0.35 6201 -
obs--92.82 %

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