[English] 日本語
Yorodumi
- PDB-4yb6: Adenosine triphosphate phosphoribosyltransferase from Campylobact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yb6
TitleAdenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni in complex with the inhibitors AMP and histidine
ComponentsATP phosphoribosyltransferase
KeywordsTRANSFERASE / Phosphoribosyltransferase / Hexamer / histidine / AMP
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. / 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
ADENOSINE MONOPHOSPHATE / HISTIDINE / DI(HYDROXYETHYL)ETHER / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 1.1Nov 1, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 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 1.3Sep 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 / pdbx_struct_conn_angle / 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 / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)206,32333
Polymers202,4486
Non-polymers3,87627
Water12,863714
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 area27770 Å2
ΔGint-190 kcal/mol
Surface area69470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.871, 124.906, 92.809
Angle α, β, γ (deg.)90.00, 115.86, 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 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLYSLYSAA4 - 2995 - 300
21ASNASNLYSLYSBB4 - 2995 - 300
12THRTHRLEULEUAA5 - 2986 - 299
22THRTHRLEULEUCC5 - 2986 - 299
13THRTHRLEULEUAA5 - 2986 - 299
23THRTHRLEULEUDD5 - 2986 - 299
14ASNASNLYSLYSAA4 - 2995 - 300
24ASNASNLYSLYSEE4 - 2995 - 300
15THRTHRLYSLYSAA5 - 2996 - 300
25THRTHRLYSLYSFF5 - 2996 - 300
16THRTHRLYSLYSBB5 - 2996 - 300
26THRTHRLYSLYSCC5 - 2996 - 300
17THRTHRLYSLYSBB5 - 2996 - 300
27THRTHRLYSLYSDD5 - 2996 - 300
18ASNASNLYSLYSBB4 - 2995 - 300
28ASNASNLYSLYSEE4 - 2995 - 300
19THRTHRLYSLYSBB5 - 2996 - 300
29THRTHRLYSLYSFF5 - 2996 - 300
110THRTHRLYSLYSCC5 - 2996 - 300
210THRTHRLYSLYSDD5 - 2996 - 300
111THRTHRLYSLYSCC5 - 2996 - 300
211THRTHRLYSLYSEE5 - 2996 - 300
112THRTHRLYSLYSCC5 - 2996 - 300
212THRTHRLYSLYSFF5 - 2996 - 300
113THRTHRLYSLYSDD5 - 2996 - 300
213THRTHRLYSLYSEE5 - 2996 - 300
114THRTHRLYSLYSDD5 - 2996 - 300
214THRTHRLYSLYSFF5 - 2996 - 300
115THRTHRLYSLYSEE5 - 2996 - 300
215THRTHRLYSLYSFF5 - 2996 - 300

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

-
Components

-
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

-
Non-polymers , 5 types, 741 molecules

#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 714 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Tris, Magnesium Chloride, PEG4000, AMP, histidine / Temp details: temperature controlled incubator

-
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: Apr 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.959 Å / Relative weight: 1
ReflectionResolution: 1.98→39.58 Å / Num. obs: 127994 / % possible obs: 98.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 2
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 3.1 / % possible all: 96.9

-
Processing

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

4yb5


Resolution: 1.98→39.58 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.067 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21477 6709 5.2 %RANDOM
Rwork0.19517 ---
obs0.19621 121691 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.844 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å2-0.55 Å2
2--1.12 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.98→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13259 0 255 714 14228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01913775
X-RAY DIFFRACTIONr_bond_other_d0.0060.0213576
X-RAY DIFFRACTIONr_angle_refined_deg1.3722.01318659
X-RAY DIFFRACTIONr_angle_other_deg1.242331170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71651772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10425.048523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64152462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1361575
X-RAY DIFFRACTIONr_chiral_restr0.0770.22247
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115356
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022793
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_it1.4562.327109
X-RAY DIFFRACTIONr_mcbond_other1.4562.327108
X-RAY DIFFRACTIONr_mcangle_it2.3023.4718874
X-RAY DIFFRACTIONr_mcangle_other2.3023.478875
X-RAY DIFFRACTIONr_scbond_it1.972.556666
X-RAY DIFFRACTIONr_scbond_other1.9692.556666
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1653.729786
X-RAY DIFFRACTIONr_long_range_B_refined4.70718.55515192
X-RAY DIFFRACTIONr_long_range_B_other4.70718.55515192
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)
11A171370.08
12B171370.08
21A172730.08
22C172730.08
31A173240.07
32D173240.07
41A169270.09
42E169270.09
51A172570.07
52F172570.07
61B172070.07
62C172070.07
71B173800.07
72D173800.07
81B167660.09
82E167660.09
91B169810.07
92F169810.07
101C172990.08
102D172990.08
111C170010.09
112E170010.09
121C171160.08
122F171160.08
131D168950.09
132E168950.09
141D171280.08
142F171280.08
151E168100.08
152F168100.08
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 469 -
Rwork0.248 8881 -
obs--97.07 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more