[English] 日本語
Yorodumi
- PDB-9b1z: Crystal structure of ADP-ribose diphosphatase from Klebsiella pne... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9b1z
TitleCrystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (Apo)
ComponentsADP-ribose pyrophosphatase
KeywordsHYDROLASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / ADP-ribose diphosphatase
Function / homology
Function and homology information


ADP-sugar diphosphatase activity / ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / nucleotide binding / metal ion binding
Similarity search - Function
Nucleoside diphosphate pyrophosphatase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (Apo)
Authors: Liu, L. / Lovell, S. / Buchko, G.W. / Battaile, K.P.
History
DepositionMar 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP-ribose pyrophosphatase
B: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5324
Polymers49,4862
Non-polymers462
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-58 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.696, 74.289, 58.021
Angle α, β, γ (deg.)90.00, 115.80, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ADP-ribose pyrophosphatase / ADP-ribose diphosphatase / ADP-ribose phosphohydrolase / Adenosine diphosphoribose pyrophosphatase


Mass: 24742.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPHS_45750 / Plasmid: KlpnC.20447.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3GVQ7, ADP-ribose diphosphatase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 33% Peg 3350, 0.1M Tris, pH 8.5, 0.2 M sodium acetate, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-102, C1. Puck: PSL-1001, Cryo: direct.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 10, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.25→45.58 Å / Num. obs: 99570 / % possible obs: 93.3 % / Redundancy: 6.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.038 / Rrim(I) all: 0.096 / Χ2: 0.91 / Net I/σ(I): 15 / Num. measured all: 609044
Reflection shellResolution: 1.25→1.28 Å / % possible obs: 55 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.441 / Num. measured all: 11802 / Num. unique obs: 4291 / CC1/2: 0.717 / Rpim(I) all: 0.302 / Rrim(I) all: 0.539 / Χ2: 0.95 / Net I/σ(I) obs: 3.1

-
Processing

Software
NameVersionClassification
PHENIX(dev_5243: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→45.58 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1455 5016 5.04 %
Rwork0.1181 --
obs0.1195 99539 93.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 2 573 3791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073423
X-RAY DIFFRACTIONf_angle_d0.9594675
X-RAY DIFFRACTIONf_dihedral_angle_d13.7011294
X-RAY DIFFRACTIONf_chiral_restr0.084523
X-RAY DIFFRACTIONf_plane_restr0.011613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.3736780.32691673X-RAY DIFFRACTION49
1.26-1.280.2598910.19161982X-RAY DIFFRACTION59
1.28-1.290.18931220.13832171X-RAY DIFFRACTION65
1.29-1.310.18271320.12992457X-RAY DIFFRACTION73
1.31-1.330.15111530.12412705X-RAY DIFFRACTION80
1.33-1.350.1821480.12522938X-RAY DIFFRACTION86
1.35-1.370.15871670.11953082X-RAY DIFFRACTION93
1.37-1.390.15461740.11623281X-RAY DIFFRACTION97
1.39-1.410.15251630.11693319X-RAY DIFFRACTION98
1.41-1.430.1441920.11373329X-RAY DIFFRACTION100
1.43-1.460.1731830.10753396X-RAY DIFFRACTION100
1.46-1.480.12942060.10023299X-RAY DIFFRACTION100
1.48-1.510.12411970.09583350X-RAY DIFFRACTION100
1.51-1.540.14141960.09353384X-RAY DIFFRACTION100
1.54-1.570.12831920.09393358X-RAY DIFFRACTION100
1.57-1.610.13121580.09733394X-RAY DIFFRACTION100
1.61-1.650.12551780.09743383X-RAY DIFFRACTION100
1.65-1.70.13231470.09723393X-RAY DIFFRACTION100
1.7-1.750.14541980.10023388X-RAY DIFFRACTION100
1.75-1.80.13011720.10463369X-RAY DIFFRACTION100
1.8-1.870.13741740.10833372X-RAY DIFFRACTION100
1.87-1.940.13851900.10863387X-RAY DIFFRACTION100
1.94-2.030.13541800.10823347X-RAY DIFFRACTION100
2.03-2.140.12571730.10393423X-RAY DIFFRACTION100
2.14-2.270.14121600.10943369X-RAY DIFFRACTION100
2.27-2.450.12121670.11593409X-RAY DIFFRACTION100
2.45-2.690.12762200.11823394X-RAY DIFFRACTION100
2.69-3.080.17561510.13223394X-RAY DIFFRACTION100
3.08-3.880.12981440.12693374X-RAY DIFFRACTION97
3.88-45.580.17252100.14363403X-RAY DIFFRACTION99

+
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