[English] 日本語
Yorodumi
- PDB-1dku: CRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dku
TitleCRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE: MOLECULAR BASIS OF ALLOSTERIC INHIBITION AND ACTIVATION.
ComponentsPROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
KeywordsTRANSFERASE / OPEN ALPHA-BETA STRUCTURE / DOMAIN DUPLICATION / PHOSPHORIBOSYLTRANSFERASE TYPE I FOLD
Function / homology
Function and homology information


ribose phosphate diphosphokinase complex / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / purine nucleotide biosynthetic process / kinase activity / phosphorylation / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phosphoribosyl pyrophosphate synthetase, conserved site / Phosphoribosyl pyrophosphate synthase signature. / Ribose-phosphate pyrophosphokinase, bacterial-type / N-terminal domain of ribose phosphate pyrophosphokinase / Phosphoribosyl synthetase-associated domain / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Rossmann fold - #2020 / Phosphoribosyltransferase-like ...Phosphoribosyl pyrophosphate synthetase, conserved site / Phosphoribosyl pyrophosphate synthase signature. / Ribose-phosphate pyrophosphokinase, bacterial-type / N-terminal domain of ribose phosphate pyrophosphokinase / Phosphoribosyl synthetase-associated domain / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHYL PHOSPHONIC ACID ADENOSINE ESTER / PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Ribose-phosphate pyrophosphokinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsEriksen, T.A. / Kadziola, A. / Bentsen, A.-K. / Harlow, K.W. / Larsen, S.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Structural basis for the function of Bacillus subtilis phosphoribosyl-pyrophosphate synthetase.
Authors: Eriksen, T.A. / Kadziola, A. / Bentsen, A.K. / Harlow, K.W. / Larsen, S.
#1: Journal: Proteins / Year: 1996
Title: Overexpression of the B. Subtilis Phosphoribosylpyrophosphate Synthetase and Crystallization of the Free Enzyme and its Substrate-Effector Complexes
Authors: Bentsen, A.-K. / Larsen, T.A. / Kadziola, A. / Larsen, S. / Harlow, K.W.
History
DepositionDec 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
B: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3616
Polymers69,8202
Non-polymers1,5414
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-11 kcal/mol
Surface area25050 Å2
MethodPISA
2
A: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
B: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
hetero molecules

A: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
B: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
hetero molecules

A: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
B: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,08418
Polymers209,4616
Non-polymers4,62312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area32980 Å2
ΔGint-85 kcal/mol
Surface area55980 Å2
MethodPISA
3
A: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
hetero molecules

B: PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3616
Polymers69,8202
Non-polymers1,5414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area6060 Å2
ΔGint-19 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.650, 115.650, 106.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein PROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE) / RIBOSE-PHOSPHATE PYROPHOSPHOKINASE


Mass: 34910.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PAB600 / Production host: Escherichia coli (E. coli) / Strain (production host): HO773, IV
References: UniProt: P14193, ribose-phosphate diphosphokinase
#2: Chemical ChemComp-AP2 / PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER


Mass: 425.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N5O9P2
#3: Chemical ChemComp-ABM / METHYL PHOSPHONIC ACID ADENOSINE ESTER / ALPHA-METHYLENE ADENOSINE MONOPHOSPHATE


Mass: 345.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N5O6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Sodium citrate, Hepes, alpha,beta-methylene ADP, Magnesium chloride, beta- octylglucoside , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
225 mMmADP1drop
350 mM1dropMgCl2
40.5 %(w/v)beta-octylglucoside1drop
51 Msodium citrate1reservoir
60.1 MHEPES1reservoir

-
Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.912
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 27, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 1.7→23 Å / Num. obs: 83506 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 4.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.037 / % possible all: 93.4
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 23 Å / Num. obs: 40252 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.35 Å / % possible obs: 98.8 % / Num. unique obs: 7158 / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.1

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
X-PLORphasing
RefinementResolution: 2.2→30 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.241 4093 SELECTED IN CONSISTENCE WITH THE R-FREE DATA FOR STRUCTURE ID CODE 1DKR
Rwork0.198 --
obs0.198 40252 -
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4544 0 100 180 4824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.011

+
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