[English] 日本語
Yorodumi
- PDB-9ojq: Crystal structure of E. coli ApaH in complex with ADP, active state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ojq
TitleCrystal structure of E. coli ApaH in complex with ADP, active state
ComponentsBis(5'-nucleosyl)-tetraphosphatase [symmetrical]
KeywordsHYDROLASE / ApaH / symmetrical hydrolase / RNA decapping
Function / homology
Function and homology information


bis(5'-nucleosyl)-tetraphosphatase activity / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) / RNA decapping / nucleobase-containing small molecule interconversion / phosphatase activity / response to X-ray / hydrolase activity / cytoplasm
Similarity search - Function
Bis(5'-nucleosyl)-tetraphosphatase, symmetrical / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNuthanakanti, A. / Serganov, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM112940 United States
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: ApaH decaps Np 4 N-capped RNAs in two alternative orientations.
Authors: Nuthanakanti, A. / Korn, M. / Levenson-Palmer, R. / Wu, Y. / Babu, N.R. / Huang, X. / Banh, R.S. / Belasco, J.G. / Serganov, A.
History
DepositionMay 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,25917
Polymers64,3212
Non-polymers1,93715
Water8,413467
1
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0108
Polymers32,1611
Non-polymers8507
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2489
Polymers32,1611
Non-polymers1,0888
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.027, 55.028, 120.182
Angle α, β, γ (deg.)90.000, 129.750, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 82 or (resid 83...
d_2ens_1(chain "B" and (resid 2 through 78 or (resid 79...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAGLYGLYAA2 - 1902 - 190
d_12LEULEUARGARGAA192 - 270192 - 270
d_21ALAALAGLYGLYBB2 - 1902 - 190
d_22LEULEUARGARGBB192 - 270192 - 270

NCS oper: (Code: givenMatrix: (-0.0253534665757, -0.0403361655952, 0.998864453005), (0.0332332378529, -0.998667368365, -0.0394846712596), (0.999125994875, 0.0321944266565, 0.0266601811294)Vector: 3. ...NCS oper: (Code: given
Matrix: (-0.0253534665757, -0.0403361655952, 0.998864453005), (0.0332332378529, -0.998667368365, -0.0394846712596), (0.999125994875, 0.0321944266565, 0.0266601811294)
Vector: 3.61785338173, -27.8209881107, 5.01496453184)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Bis(5'-nucleosyl)-tetraphosphatase [symmetrical] / Ap4A hydrolase / Diadenosine 5' / 5'''-P1 / P4-tetraphosphate pyrophosphohydrolase / Diadenosine ...Ap4A hydrolase / Diadenosine 5' / 5'''-P1 / P4-tetraphosphate pyrophosphohydrolase / Diadenosine tetraphosphatase


Mass: 32160.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: apaH, b0049, JW0048 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P05637, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)

-
Non-polymers , 6 types, 482 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Conditions: 0.3 mM ApaH (10 mg/mL), 1 mM DTT, 4 mM MgCl2, 10 mM Ca(OAc)2, 25 mM Hepes (pH 7.5), 0.2 M NaCl. Well solution: 0.1 M Hepes (pH 7.5), 0.2 M Li2SO4, 25% PEG3350.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2→32.27 Å / Num. obs: 56473 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 26.95 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.215 / Net I/σ(I): 4.8
Reflection shellResolution: 2→2.04 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.633 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2839 / CC1/2: 0.337 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→32.27 Å / SU ML: 0.2834 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0282
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2468 2895 5.14 %
Rwork0.204 53416 -
obs0.2062 56311 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.4 Å2
Refinement stepCycle: LAST / Resolution: 2→32.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4210 0 105 467 4782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814437
X-RAY DIFFRACTIONf_angle_d0.95826063
X-RAY DIFFRACTIONf_chiral_restr0.0534645
X-RAY DIFFRACTIONf_plane_restr0.0069771
X-RAY DIFFRACTIONf_dihedral_angle_d9.0152598
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.518152924937 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.34131360.29362479X-RAY DIFFRACTION96.71
2.04-2.070.34671410.28422429X-RAY DIFFRACTION97.9
2.07-2.110.31941480.27632506X-RAY DIFFRACTION98.81
2.11-2.150.30191460.26452538X-RAY DIFFRACTION99.37
2.15-2.190.31911440.25962526X-RAY DIFFRACTION99.52
2.19-2.240.30181160.262518X-RAY DIFFRACTION99.32
2.24-2.290.33431550.26882553X-RAY DIFFRACTION99.45
2.29-2.350.29531430.24192487X-RAY DIFFRACTION99.62
2.35-2.420.25881620.22912520X-RAY DIFFRACTION99.78
2.42-2.490.27611420.21422546X-RAY DIFFRACTION99.63
2.49-2.570.27471530.21612514X-RAY DIFFRACTION99.74
2.57-2.660.25461380.20872559X-RAY DIFFRACTION99.89
2.66-2.760.24711290.20162566X-RAY DIFFRACTION99.81
2.77-2.890.2551140.1992546X-RAY DIFFRACTION99.7
2.89-3.040.25611300.19832588X-RAY DIFFRACTION99.82
3.04-3.230.21661340.18952575X-RAY DIFFRACTION99.74
3.23-3.480.25081160.1942565X-RAY DIFFRACTION99.48
3.48-3.830.21391320.17542559X-RAY DIFFRACTION99.45
3.83-4.390.19131140.1682610X-RAY DIFFRACTION99.31
4.39-5.520.21961400.17362588X-RAY DIFFRACTION99.38
5.52-32.270.19991620.18812644X-RAY DIFFRACTION99.68

+
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