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- PDB-5m8h: ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter a... -

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Basic information

Entry
Database: PDB / ID: 5m8h
TitleATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter arcticus
Components
  • ATP phosphoribosyltransferase
  • ATP phosphoribosyltransferase regulatory subunit
KeywordsTRANSFERASE / HisGZ / ATPPRT / complex / octameric
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / 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 ...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) / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
STRONTIUM ION / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase regulatory subunit
Similarity search - Component
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.34 Å
AuthorsAlphey, M.S. / Ge, Y. / Naismith, J.H. / da Silva, R.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
University of St. Andrews United Kingdom
CitationJournal: Biochemistry / Year: 2017
Title: Kinetics and Structure of a Cold-Adapted Hetero-Octameric ATP Phosphoribosyltransferase.
Authors: Stroek, R. / Ge, Y. / Talbot, P.D. / Glok, M.K. / Bernas, K.E. / Thomson, C.M. / Gould, E.R. / Alphey, M.S. / Liu, H. / Florence, G.J. / Naismith, J.H. / da Silva, R.G.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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_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 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)276,30645
Polymers273,4808
Non-polymers2,82637
Water11,331629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35290 Å2
ΔGint-661 kcal/mol
Surface area96240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.020, 146.730, 101.900
Angle α, β, γ (deg.)90.000, 102.400, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27F
18E
28G
19E
29H
110F
210G
111F
211H
112G
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYVALVALAA0 - 3871 - 388
21GLYGLYVALVALBB0 - 3871 - 388
12METMETVALVALAA1 - 3872 - 388
22METMETVALVALCC1 - 3872 - 388
13GLYGLYVALVALAA0 - 3871 - 388
23GLYGLYVALVALDD0 - 3871 - 388
14METMETALAALABB1 - 3862 - 387
24METMETALAALACC1 - 3862 - 387
15GLYGLYVALVALBB0 - 3871 - 388
25GLYGLYVALVALDD0 - 3871 - 388
16METMETALAALACC1 - 3862 - 387
26METMETALAALADD1 - 3862 - 387
17PHEPHEILEILEEE21 - 22722 - 228
27PHEPHEILEILEFF21 - 22722 - 228
18PHEPHESERSEREE21 - 22622 - 227
28PHEPHESERSERGG21 - 22622 - 227
19PHEPHEILEILEEE21 - 22722 - 228
29PHEPHEILEILEHH21 - 22722 - 228
110PHEPHESERSERFF21 - 22622 - 227
210PHEPHESERSERGG21 - 22622 - 227
111GLUGLUASNASNFF20 - 22821 - 229
211GLUGLUASNASNHH20 - 22821 - 229
112PHEPHESERSERGG21 - 22622 - 227
212PHEPHESERSERHH21 - 22622 - 227

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
ATP phosphoribosyltransferase regulatory subunit


Mass: 43129.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: some residues missing from model due to flexibility/poor electron density
Source: (gene. exp.) Psychrobacter arcticus (strain DSM 17307 / 273-4) (bacteria)
Gene: hisZ, Psyc_0676 / Plasmid: pJexpress414 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4FTX3
#2: Protein
ATP phosphoribosyltransferase / ATP-PRTase


Mass: 25240.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Residues missing in model at N- and C-termini due to flexible regions not seen in electron density
Source: (gene. exp.) Psychrobacter arcticus (strain DSM 17307 / 273-4) (bacteria)
Gene: hisG, Psyc_1903 / Plasmid: pJexpress431 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q4FQF7, ATP phosphoribosyltransferase

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Non-polymers , 4 types, 666 molecules

#3: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Sr
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 11% PEG3350, 0.1M bicine pH8.5, 0.15M strontium chloride, 0.15M potassium bromide, 4% 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 5, 2016 / Details: varimax mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.34→30.63 Å / Num. obs: 110587 / % possible obs: 97.6 % / Redundancy: 3.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.135 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.34-2.382.40.9690.366181
12.82-30.633.70.0420.998193

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VD2, 3OD1

2vd2

3od1


Resolution: 2.34→30.63 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / SU B: 13.419 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.274
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 5467 4.9 %RANDOM
Rwork0.2274 ---
obs0.2295 105092 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 139.2 Å2 / Biso mean: 47.653 Å2 / Biso min: 3.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20.34 Å2
2---0.22 Å20 Å2
3---1.68 Å2
Refinement stepCycle: final / Resolution: 2.34→30.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18206 0 121 629 18956
Biso mean--50.89 35.8 -
Num. residues----2343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01918619
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218312
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.97525257
X-RAY DIFFRACTIONr_angle_other_deg0.943341914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13452335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53724.168847
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29153201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0115132
X-RAY DIFFRACTIONr_chiral_restr0.0770.22967
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024223
X-RAY DIFFRACTIONr_mcbond_it2.9754.6379364
X-RAY DIFFRACTIONr_mcbond_other2.9744.6379363
X-RAY DIFFRACTIONr_mcangle_it4.7386.94611685
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A229380.08
12B229380.08
21A228960.08
22C228960.08
31A233800.06
32D233800.06
41B234080.06
42C234080.06
51B231480.08
52D231480.08
61C230520.07
62D230520.07
71E122040.08
72F122040.08
81E122520.06
82G122520.06
91E122220.07
92H122220.07
101F121500.07
102G121500.07
111F124600.06
112H124600.06
121G121460.07
122H121460.07
LS refinement shellResolution: 2.341→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 356 -
Rwork0.368 6517 -
all-6873 -
obs--82.66 %

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