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- PDB-8oy0: ATP phosphoribosyltransferase (HisZG ATPPRT) from Acinetobacter b... -

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Basic information

Entry
Database: PDB / ID: 8oy0
TitleATP phosphoribosyltransferase (HisZG ATPPRT) from Acinetobacter baumanii
Components
  • ATP phosphoribosyltransferase
  • ATP phosphoribosyltransferase regulatory subunit
KeywordsTRANSFERASE / ATPPRT / HisZG / histidine / biosynthesis
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / glycosyltransferase activity / 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
ATP phosphoribosyltransferase regulatory subunit / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 17978 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAlphey, M.S. / Read, B. / da Silva, R.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M010996/1 United Kingdom
CitationJournal: Biochemistry / Year: 2024
Title: Crystal Structure, Steady-State, and Pre-Steady-State Kinetics of Acinetobacter baumannii ATP Phosphoribosyltransferase.
Authors: Read, B.J. / Cadzow, A.F. / Alphey, M.S. / Mitchell, J.B.O. / da Silva, R.G.
History
DepositionMay 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: 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

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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 regulatory subunit
D: ATP phosphoribosyltransferase regulatory subunit
E: ATP phosphoribosyltransferase
F: ATP phosphoribosyltransferase
G: ATP phosphoribosyltransferase
H: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,70713
Polymers272,5238
Non-polymers1845
Water4,630257
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32950 Å2
ΔGint-175 kcal/mol
Surface area90370 Å2
Unit cell
Length a, b, c (Å)80.271, 172.821, 98.109
Angle α, β, γ (deg.)90.00, 90.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ATP phosphoribosyltransferase regulatory subunit


Mass: 42960.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The initial Gly remains after cleavage of a purification tag
Source: (gene. exp.) Acinetobacter baumannii ATCC 17978 (bacteria)
Gene: hisZ / Plasmid: pJexpress414 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A059ZNW9
#2: Protein
ATP phosphoribosyltransferase


Mass: 25170.256 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The initial Gly remains after cleavage of a purification tag
Source: (gene. exp.) Acinetobacter baumannii ATCC 17978 (bacteria)
Gene: hisG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V5VGC6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M sodium nitrate, 0.1M bis-Tris propane pH 8.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 27, 2021 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.4→30.82 Å / Num. obs: 99446 / % possible obs: 95.6 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.051 / Rrim(I) all: 0.135 / Χ2: 0.99 / Net I/σ(I): 9.6 / Num. measured all: 631956
Reflection shellResolution: 2.4→2.44 Å / % possible obs: 80.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 1.045 / Num. measured all: 19967 / Num. unique obs: 4130 / CC1/2: 0.618 / Rpim(I) all: 0.498 / Rrim(I) all: 1.164 / Χ2: 0.86 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30.82 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.912 / SU B: 23.636 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 0.548 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26424 5033 5.1 %RANDOM
Rwork0.23826 ---
obs0.23959 94223 95.3 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.623 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å20 Å2-0.38 Å2
2--0.75 Å20 Å2
3----3.98 Å2
Refinement stepCycle: 1 / Resolution: 2.4→30.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17980 0 10 257 18247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01218289
X-RAY DIFFRACTIONr_bond_other_d0.0010.01617671
X-RAY DIFFRACTIONr_angle_refined_deg0.9311.64224829
X-RAY DIFFRACTIONr_angle_other_deg0.3241.56940495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48252318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.3665111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.753103032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0450.22903
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0221420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024020
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_it0.9962.1119359
X-RAY DIFFRACTIONr_mcbond_other0.9962.1119359
X-RAY DIFFRACTIONr_mcangle_it1.723.78611648
X-RAY DIFFRACTIONr_mcangle_other1.723.78611649
X-RAY DIFFRACTIONr_scbond_it1.0252.1988930
X-RAY DIFFRACTIONr_scbond_other1.0252.1988931
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7644.00813182
X-RAY DIFFRACTIONr_long_range_B_refined3.55119.3819622
X-RAY DIFFRACTIONr_long_range_B_other3.55119.3819623
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 315 -
Rwork0.315 5904 -
obs--81.56 %
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)
11.073-0.15340.14691.4979-0.01380.7149-0.1455-0.16410.11140.38590.12590.119-0.101-0.28670.01960.22780.08010.02670.133-0.00950.30985.04483.15450.965
20.80990.10950.11221.32260.2751.0351-0.09020.0946-0.23010.16140.1474-0.53570.26720.096-0.05730.20390.0341-0.07210.0326-0.05310.528628.99665.68544.706
30.908-0.1292-0.01130.91270.33350.8128-0.12770.04570.2439-0.17220.1545-0.2849-0.19630.0664-0.02680.2272-0.05370.06250.04990.03340.441929.512101.9226.668
40.99690.1505-0.09821.3766-0.10730.9295-0.17940.2764-0.1252-0.38660.13130.1720.1048-0.2760.04810.2833-0.099-0.00640.15370.00540.32436.13182.918-1.163
50.8288-0.0213-0.43650.879-0.25124.2825-0.073-0.07140.24070.20910.00040.0045-0.44480.02950.07260.2670.1112-0.02410.0714-0.01790.42774.357115.42742.503
61.31890.3354-0.27772.8692-1.61242.51630.0395-0.05020.38840.33830.0787-0.0045-0.4364-0.0095-0.11820.22850.0335-0.0510.0139-0.06730.580828.816118.87435.293
70.8037-0.3301-0.21452.9292-1.73693.1988-0.11890.1911-0.2415-0.49660.0838-0.19080.74210.08660.03510.3473-0.01890.11210.0879-0.13330.513531.41148.28815.821
80.6858-0.12240.46620.89010.18954.8777-0.03280.1595-0.2486-0.17270.04460.04830.34110.122-0.01180.3169-0.15310.02550.1137-0.06760.40456.82650.5857.502
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 389
2X-RAY DIFFRACTION2B6 - 386
3X-RAY DIFFRACTION3C5 - 389
4X-RAY DIFFRACTION4D5 - 389
5X-RAY DIFFRACTION5E5 - 226
6X-RAY DIFFRACTION6F8 - 225
7X-RAY DIFFRACTION7G8 - 225
8X-RAY DIFFRACTION8H8 - 226

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