[English] 日本語
Yorodumi
- PDB-6qva: Crystal structure of a CHAD domain from Chlorobium tepidum in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qva
TitleCrystal structure of a CHAD domain from Chlorobium tepidum in complex with inorganic polyphosphate
ComponentsCHAD domain
KeywordsNUCLEAR PROTEIN / four-helix bundle / inorganic polyphosphate binding protein / all alpha-helical protein
Function / homology
Function and homology information


CHAD domain / CHAD domain / CHAD domain superfamily / CHAD / CHAD domain / CHAD domain / CHAD domain profile. / Alpha solenoid / Mainly Alpha
Similarity search - Domain/homology
TRIPHOSPHATE / Chem-9PI / PHOSPHATE ION / CHAD domain-containing protein
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLorenzo-Orts, L. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Research Council310856 Switzerland
CitationJournal: Life Sci Alliance / Year: 2019
Title: Molecular characterization of CHAD domains as inorganic polyphosphate-binding modules.
Authors: Lorenzo-Orts, L. / Hohmann, U. / Zhu, J. / Hothorn, M.
History
DepositionMar 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHAD domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5888
Polymers36,2491
Non-polymers1,3397
Water1,22568
1
A: CHAD domain
hetero molecules

A: CHAD domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,17716
Polymers72,4992
Non-polymers2,67814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area3680 Å2
ΔGint-15 kcal/mol
Surface area31230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.400, 97.031, 106.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein CHAD domain


Mass: 36249.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
Gene: CT0884 / Plasmid: pMH-HT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8KE09

-
Non-polymers , 5 types, 75 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-9PI / bis[oxidanyl-[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxy-phosphoryl] hydrogen phosphate


Mass: 737.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H11O28P9
#4: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.4 M (NH4)3PO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999856 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999856 Å / Relative weight: 1
ReflectionResolution: 2.05→19.7 Å / Num. obs: 22776 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 13.3 % / Biso Wilson estimate: 46.1 Å2 / CC1/2: 1 / Rrim(I) all: 0.155 / Rsym value: 0.149 / Net I/σ(I): 14.1
Reflection shellResolution: 2.05→2.17 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 3576 / CC1/2: 0.43 / Rrim(I) all: 2.35 / Rsym value: 2.26 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3e0s

3e0s


Resolution: 2.05→19.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 15.427 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.188 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25483 1127 5 %RANDOM
Rwork0.20767 ---
obs0.20997 21397 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.982 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--1.57 Å20 Å2
3----1.77 Å2
Refinement stepCycle: 1 / Resolution: 2.05→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 71 68 2632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132632
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172470
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.6813562
X-RAY DIFFRACTIONr_angle_other_deg1.2261.5785703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1335317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.2520.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48415473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7361531
X-RAY DIFFRACTIONr_chiral_restr0.0640.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022883
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02594
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.863.6841247
X-RAY DIFFRACTIONr_mcbond_other1.8593.6821246
X-RAY DIFFRACTIONr_mcangle_it2.5295.5161559
X-RAY DIFFRACTIONr_mcangle_other2.5285.5171560
X-RAY DIFFRACTIONr_scbond_it3.3074.381382
X-RAY DIFFRACTIONr_scbond_other2.8734.1211331
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4446.0181911
X-RAY DIFFRACTIONr_long_range_B_refined8.5873.85210975
X-RAY DIFFRACTIONr_long_range_B_other8.41872.24710851
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.051→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 82 -
Rwork0.413 1555 -
obs--99.21 %
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)
17.13323.1533-2.07857.4677-0.03463.5569-0.37160.7161-0.4971-0.28590.18920.22330.4339-0.67380.18250.0956-0.05680.00150.1778-0.06730.071919.5838-1.59668.6066
25.5701-0.3581-1.52480.64420.6961.9009-0.03920.1596-0.0638-0.0189-0.0830.1851-0.026-0.25980.12220.00520.0021-0.01110.0375-0.00870.069613.209312.213516.6264
33.8008-0.6842-3.74560.8297-0.51826.99470.07170.16130.0286-0.15380.0151-0.00670.0269-0.2995-0.08680.04980.0071-0.0130.0198-0.01860.078-1.683720.521733.4348
47.4057-4.4364-0.79593.88470.29131.25280.02110.1351-0.06760.0216-0.0770.1242-0.2715-0.19580.0560.07830.0188-0.01920.06760.0040.022921.018314.80767.8808
50.93140.4764-0.66280.6602-1.276611.9364-0.0222-0.17680.04280.05740.0249-0.05170.03760.3535-0.00270.03740.03510.01050.1007-0.00960.104227.0888-3.335326.6165
62.71130.3322-1.04453.33122.69516.25260.0044-0.3026-0.14360.238-0.01080.00120.02970.02150.00630.02740.00890.01910.03970.03370.147917.1437-1.714928.8209
72.3631-3.143-1.93155.32193.11972.3824-0.0243-0.1001-0.18340.03290.00090.0390.17420.07430.02340.04510.0122-0.00640.05730.03010.05259.83516.280341.0243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A207 - 224
2X-RAY DIFFRACTION2A225 - 287
3X-RAY DIFFRACTION3A288 - 342
4X-RAY DIFFRACTION4A343 - 373
5X-RAY DIFFRACTION5A374 - 397
6X-RAY DIFFRACTION6A398 - 438
7X-RAY DIFFRACTION7A439 - 521

+
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