[English] 日本語
Yorodumi
- PDB-9r98: DhhP of Borrelia burgdorferi in complex with AMP (SAD/Fe) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r98
TitleDhhP of Borrelia burgdorferi in complex with AMP (SAD/Fe)
ComponentsDHH family
KeywordsHYDROLASE / phosphodiesterase / c-di-AMP / cyclic di-AMP / heterobimetallic
Function / homology
Function and homology information


nucleic acid binding
Similarity search - Function
: / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / : / DHH family
Similarity search - Component
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKlima, M. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: DhhP of Borrelia burgdorferi in complex with AMP (SAD/Fe)
Authors: Klima, M. / Boura, E.
History
DepositionMay 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DHH family
B: DHH family
C: DHH family
D: DHH family
E: DHH family
F: DHH family
G: DHH family
H: DHH family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,54828
Polymers293,2738
Non-polymers2,27520
Water18010
1
A: DHH family
B: DHH family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8877
Polymers73,3182
Non-polymers5695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-78 kcal/mol
Surface area27560 Å2
2
C: DHH family
D: DHH family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8877
Polymers73,3182
Non-polymers5695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-75 kcal/mol
Surface area27590 Å2
3
E: DHH family
F: DHH family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8877
Polymers73,3182
Non-polymers5695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-74 kcal/mol
Surface area27330 Å2
4
G: DHH family
H: DHH family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8877
Polymers73,3182
Non-polymers5695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-76 kcal/mol
Surface area27410 Å2
Unit cell
Length a, b, c (Å)74.790, 80.410, 132.800
Angle α, β, γ (deg.)91.100, 91.330, 92.700
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein
DHH family


Mass: 36659.094 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Gene: BB_0619 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O51564
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% v/v PEG 500 MME; 10% w/v PEG 20.000; 100mM Gly-Gly/AMPD pH 8.5; 0.3% w/v CHAPS; 0.3% w/v CHAPSO; 0.3% w/v Sodium glycocholate hydrate; 0.3% w/v Taurocholic acid sodium salt hydrate; 3% DMSO

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.735 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Apr 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.735 Å / Relative weight: 1
ReflectionResolution: 3.3→49.05 Å / Num. obs: 89842 / % possible obs: 96.59 % / Redundancy: 3.4 % / Biso Wilson estimate: 77.66 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1177 / Rpim(I) all: 0.07402 / Rrim(I) all: 0.1396 / Net I/σ(I): 11.34
Reflection shellResolution: 3.3→3.418 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5454 / Mean I/σ(I) obs: 3.62 / Num. unique obs: 9079 / CC1/2: 0.844 / CC star: 0.957 / Rpim(I) all: 0.335 / Rrim(I) all: 0.6419 / % possible all: 96.74

-
Processing

Software
NameVersionClassification
XDSbuilt 20241002data reduction
XDSbuilt 20241002data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
Coot0.9.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→49.05 Å / SU ML: 0.353 / Cross valid method: FREE R-VALUE / σ(F): 0.79 / Phase error: 22.6478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 4489 5 %random selection
Rwork0.1757 85316 --
obs0.1772 89805 96.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.15 Å2
Refinement stepCycle: LAST / Resolution: 3.3→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20431 0 108 10 20549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002920952
X-RAY DIFFRACTIONf_angle_d0.555828225
X-RAY DIFFRACTIONf_chiral_restr0.04313121
X-RAY DIFFRACTIONf_plane_restr0.00383576
X-RAY DIFFRACTIONf_dihedral_angle_d10.10717788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.340.33461550.29652928X-RAY DIFFRACTION97.32
3.34-3.380.30621460.27162778X-RAY DIFFRACTION96.25
3.38-3.420.31761530.26062915X-RAY DIFFRACTION96.54
3.42-3.460.27991490.2522831X-RAY DIFFRACTION98.41
3.46-3.510.27451520.25462884X-RAY DIFFRACTION96.32
3.51-3.550.27611490.23882803X-RAY DIFFRACTION95.72
3.55-3.610.26061530.22932884X-RAY DIFFRACTION97.9
3.61-3.660.23511510.22752845X-RAY DIFFRACTION97.21
3.66-3.720.23541460.22282802X-RAY DIFFRACTION95.78
3.72-3.780.25431500.21952829X-RAY DIFFRACTION96.53
3.78-3.840.2661530.22662887X-RAY DIFFRACTION96.63
3.84-3.910.24661420.20572725X-RAY DIFFRACTION93.33
3.91-3.990.21281480.22782X-RAY DIFFRACTION95.81
3.99-4.070.26361510.18962849X-RAY DIFFRACTION96.65
4.07-4.160.24141530.1762890X-RAY DIFFRACTION95.81
4.16-4.250.20181460.17132826X-RAY DIFFRACTION98.74
4.25-4.360.17761490.16382850X-RAY DIFFRACTION96.62
4.36-4.480.20931530.15692906X-RAY DIFFRACTION96.87
4.48-4.610.16341500.1512811X-RAY DIFFRACTION97.27
4.61-4.760.17191510.14642836X-RAY DIFFRACTION96.79
4.76-4.930.17211510.14462902X-RAY DIFFRACTION97.23
4.93-5.130.20531490.15132824X-RAY DIFFRACTION96.28
5.13-5.360.18821480.15252874X-RAY DIFFRACTION96
5.36-5.640.20421470.17292806X-RAY DIFFRACTION97.14
5.64-5.990.18671470.18192852X-RAY DIFFRACTION96.87
5.99-6.460.21581510.17852861X-RAY DIFFRACTION97.48
6.46-7.10.21571500.17992870X-RAY DIFFRACTION97.8
7.1-8.130.19391540.15452887X-RAY DIFFRACTION97.47
8.13-10.220.12571510.11542793X-RAY DIFFRACTION94.6
10.23-49.050.13111410.11932786X-RAY DIFFRACTION95.22

+
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