[English] 日本語
Yorodumi
- PDB-10xf: Corynebacterium bovis DnaA DI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 10xf
TitleCorynebacterium bovis DnaA DI
ComponentsChromosomal replication initiator protein DnaA
KeywordsDNA BINDING PROTEIN / Initiator
Function / homology
Function and homology information


regulation of DNA replication / DNA replication origin binding / DNA replication initiation / lipid binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Bacterial dnaA protein helix-turn-helix / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / Trp repressor/replication initiator / ATPases associated with a variety of cellular activities ...DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Bacterial dnaA protein helix-turn-helix / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / Trp repressor/replication initiator / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesCorynebacterium bovis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEllis, P.K. / Schumacher, M.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
National Science Foundation (NSF, United States)DGE 2139754 United States
CitationJournal: To Be Published
Title: Structures reveal DnaA domain I dimer conserved across Actinomycetes: implications for replication initiation
Authors: Ellis, P.K. / Schumacher, M.A.
History
DepositionFeb 11, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chromosomal replication initiator protein DnaA


Theoretical massNumber of molelcules
Total (without water)10,3651
Polymers10,3651
Non-polymers00
Water1,54986
1
A: Chromosomal replication initiator protein DnaA

A: Chromosomal replication initiator protein DnaA


Theoretical massNumber of molelcules
Total (without water)20,7302
Polymers20,7302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_545x-y,-y-1,-z1
Unit cell
Length a, b, c (Å)58.577, 58.577, 93.706
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

-
Components

#1: Protein Chromosomal replication initiator protein DnaA


Mass: 10364.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium bovis (bacteria) / Gene: dnaA, CXF48_06640 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3R8VTP7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.0 M Ammonium Citrate dibasic; 0.1 M Sodium Acetate trihydrate, pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 24, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.8→22.31 Å / Num. obs: 9348 / % possible obs: 99.9 % / Redundancy: 22.6 % / Biso Wilson estimate: 21.41 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.022 / Rrim(I) all: 0.106 / Net I/σ(I): 23.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 22.3 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 546 / CC1/2: 0.929 / Rpim(I) all: 0.258 / Rrim(I) all: 1.257 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→21.37 Å / SU ML: 0.2401 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1037
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2273 928 9.98 %
Rwork0.1881 8366 -
obs0.1919 9294 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.71 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms678 0 0 86 764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036724
X-RAY DIFFRACTIONf_angle_d0.72411003
X-RAY DIFFRACTIONf_chiral_restr0.047126
X-RAY DIFFRACTIONf_plane_restr0.0102129
X-RAY DIFFRACTIONf_dihedral_angle_d12.3188274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.890.41721280.3181158X-RAY DIFFRACTION98.54
1.9-2.010.26131280.23021154X-RAY DIFFRACTION99.3
2.01-2.170.2361300.19351170X-RAY DIFFRACTION99.92
2.17-2.390.26021300.19221169X-RAY DIFFRACTION99.54
2.39-2.730.22061330.18411190X-RAY DIFFRACTION99.55
2.73-3.440.22221350.18581218X-RAY DIFFRACTION99.49
3.44-21.370.18931440.16411307X-RAY DIFFRACTION99.79
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.388243818260.03872587177220.04814644780646.14771398372-1.068841675685.98649774584-0.04151916191690.1709782617790.8202333712810.0138378105939-0.1391121689910.0481995945163-0.392710116663-0.1570606061680.1859725937320.1694385891860.000530642107236-0.07451569651140.240559445317-0.0008208048904040.21230363798-5.32059963484-19.5120561672-5.58230464922
20.546086571942-1.277814395320.2094324087854.92843298592-2.846946645422.94952195358-0.02065829651110.3627784696530.363944830023-0.416042322442-0.598732569092-1.0544167160.2457568802920.7115427170840.5324603276020.2702829284750.05304502829810.0816545790790.4236442230890.2127711160840.3150962276076.2129768423-21.0974734848-8.68315702789
35.82916922639-0.8234341411811.053626432435.495901976551.832302014750.920293903191-0.194941214501-0.0787838959691-0.00340807962289-0.002485723413810.0190212628893-0.05819997808060.103405823-0.0005653351841380.19893675720.09975682202910.00480765653944-0.01320235750.1089546153160.0265244445710.08915693776810.487737590352-30.47621491742.64348957556
48.04207430427-5.40779506255-4.416948268763.870703507513.813940402387.41278872991-0.15904250737-0.2234783144940.6537114591980.2250178542120.203974644885-0.792746299084-0.1832758857990.992736219621-0.07536589009180.163039070485-0.0169226162665-0.03975361099190.313238821469-0.02492115533350.2128150691111.2911534565-22.62212486680.858410136539
56.864978090813.96430900643-3.486868619866.960999675060.4245087378964.98614236613-0.147010001362-0.4019726946640.7941417778970.0316938304-0.04864244919390.00606065639564-0.37071610773-0.1174318755180.1938265215790.1992257330970.0356120473216-0.100410068760.180954740035-0.02380549963140.245429482766-3.74167343515-18.0264304463.64368215285
64.72201241674-4.93192747719-3.116234995397.878042562321.8646737375.71543738176-0.1752960595490.345077226862-0.560914677966-0.0935457487289-0.4360106717440.4434483741980.0250886150791-0.1125812052810.4759793829980.134606483651-0.00557029657298-0.04457764320440.18908449249-0.04083195388550.1654371090971.13069666791-27.13131838765.7039214907
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 33 )5 - 331 - 29
22chain 'A' and (resid 34 through 42 )34 - 4230 - 38
33chain 'A' and (resid 43 through 59 )43 - 5939 - 55
44chain 'A' and (resid 60 through 70 )60 - 7056 - 66
55chain 'A' and (resid 71 through 82 )71 - 8267 - 78
66chain 'A' and (resid 83 through 93 )83 - 9379 - 89

+
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