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- PDB-5ub9: Catalytic core domain of Adenosine triphosphate phosphoribosyltra... -

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Basic information

Entry
Database: PDB / ID: 5ub9
TitleCatalytic core domain of Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni
ComponentsATP phosphoribosyltransferase
KeywordsTRANSFERASE / Histidine-biosynthesis / HisG
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 / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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.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_label_asym_id / _struct_conn.ptnr2_symmetry

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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)51,14210
Polymers50,6812
Non-polymers4618
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-49 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.697, 79.926, 91.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ATP phosphoribosyltransferase / ATP-PRTase


Mass: 25340.268 Da / Num. of mol.: 2 / Fragment: residues 1-225
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.36 Å3/Da / Density % sol: 47.94 % / Description: octahedral crystal shape
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, crystals grow from precipitate
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: Jul 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.959 Å / Relative weight: 1
ReflectionResolution: 1.9→39.96 Å / Num. obs: 38485 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 4.6 / CC1/2: 0.956 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: truncated chain of PDB 4YB5

4yb5


Resolution: 1.9→39.96 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.277 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24257 989 2.6 %RANDOM
Rwork0.19318 ---
obs0.19445 37437 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.39 Å2
Baniso -1Baniso -2Baniso -3
1-14.36 Å20 Å20 Å2
2---10.4 Å2-0 Å2
3----3.95 Å2
Refinement stepCycle: 1 / Resolution: 1.9→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3316 0 23 295 3634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193428
X-RAY DIFFRACTIONr_bond_other_d0.0010.023363
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9964634
X-RAY DIFFRACTIONr_angle_other_deg0.81537722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.835446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.82625.135148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05315628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5231523
X-RAY DIFFRACTIONr_chiral_restr0.0880.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023933
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02722
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_it1.0981.4131777
X-RAY DIFFRACTIONr_mcbond_other1.0711.4041771
X-RAY DIFFRACTIONr_mcangle_it1.692.0962222
X-RAY DIFFRACTIONr_mcangle_other1.6892.0982223
X-RAY DIFFRACTIONr_scbond_it1.4651.581651
X-RAY DIFFRACTIONr_scbond_other1.4651.5821652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3222.3062413
X-RAY DIFFRACTIONr_long_range_B_refined5.98612.3913977
X-RAY DIFFRACTIONr_long_range_B_other5.98612.3993978
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 80 -
Rwork0.294 2699 -
obs--99.53 %
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)
10.6185-0.0917-0.25881.0535-0.17341.19320.0110.0477-0.10190.07580.00090.2103-0.021-0.0215-0.01190.0640.00140.00730.0842-0.02770.1373-0.9379-12.14329.4383
20.8740.6129-0.13871.6378-0.30950.41330.1473-0.0488-0.03320.4319-0.094-0.126-0.08250.1248-0.05330.1858-0.0271-0.04730.09680.00110.045915.6857-14.930327.4023
38.1621-2.0083-0.68774.3519-0.27572.00710.2745-0.2936-0.20011.1599-0.1205-0.004-0.1315-0.1023-0.1540.4309-0.0991-0.03760.09130.04130.02787.6362-22.772448.762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 225
2X-RAY DIFFRACTION2B5 - 200
3X-RAY DIFFRACTION3B201 - 219

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