[English] 日本語
Yorodumi
- PDB-3h7m: Crystal Structure of a Histidine Kinase Sensor Domain with Simila... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h7m
TitleCrystal Structure of a Histidine Kinase Sensor Domain with Similarity to Periplasmic Binding Proteins
ComponentsSensor protein
KeywordsTRANSFERASE / histidine kinase sensor domain / Kinase / Phosphoprotein
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020
Similarity search - Function
Bacterial periplasmic substrate-binding proteins / His Kinase A (phospho-acceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Bacterial periplasmic substrate-binding proteins / His Kinase A (phospho-acceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Periplasmic binding protein-like II / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsCheung, J. / Le-Khac, M. / Hendrickson, W.A.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of a histidine kinase sensor domain with similarity to periplasmic binding proteins.
Authors: Cheung, J. / Le-Khac, M. / Hendrickson, W.A.
History
DepositionApr 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9852
Polymers25,9621
Non-polymers231
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.920, 122.920, 81.692
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Sensor protein


Mass: 25961.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: GSU2755 / Plasmid: pGEX4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q749I7, histidine kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.43 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: isopropanol, PEG3350, calcium acetate, pH 6.0, vapor diffusion, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9870, 0.9795, 0.9791, 0.9715
DetectorDetector: CCD / Date: Sep 23, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9871
20.97951
30.97911
40.97151
ReflectionRedundancy: 6.3 % / Av σ(I) over netI: 16.2 / Number: 96529 / Rmerge(I) obs: 0.057 / Χ2: 1.02 / D res high: 2.9 Å / D res low: 20 Å / Num. obs: 15305 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.192010010.0361.0199.3
4.946.1910010.0541.0369.2
4.324.9410010.051.0048
3.934.3210010.0531.0066.4
3.653.9399.810.0591.0195.2
3.443.6599.910.0761.045.2
3.263.4499.910.1121.0265.2
3.123.2610010.1621.0075.1
33.1299.910.2411.0354.9
2.9398.110.2831.0364.4
ReflectionResolution: 2.4→20 Å / Num. obs: 14718 / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.046 / Χ2: 1.03 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.494.20.41914341.05399.9
2.49-2.584.30.33114381.053100
2.58-2.74.30.24714251.035100
2.7-2.844.30.17114601.021100
2.84-3.024.30.11614441.03399.9
3.02-3.254.40.08714591.0299.9
3.25-3.584.70.05914591.04299.8
3.58-4.095.60.04314921.022100
4.09-5.147.10.03415030.99499.9
5.14-207.20.03116041.047100

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
CNS1.1refinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.87 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1761706.125 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.285 735 5 %RANDOM
Rwork0.228 ---
obs-14682 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.846 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso mean: 55.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.99 Å22.06 Å20 Å2
2---2.99 Å20 Å2
3---5.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 1 141 1951
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it4.171.5
X-RAY DIFFRACTIONc_mcangle_it5.952
X-RAY DIFFRACTIONc_scbond_it6.562
X-RAY DIFFRACTIONc_scangle_it8.362.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 108 4.5 %
Rwork0.306 2280 -
all-2388 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramion.top
X-RAY DIFFRACTION3ion.paramwater.top

+
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://pdbjlvh1.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