5FQ1

Structure of the cytoplasmic PAS domain of the Geobacillus thermodenitrificans histidine kinase CitA

> Summary

Summary for 5FQ1

DescriptorHISTIDINE KINASE (E.C.2.7.13.3)
Functional Keywordstransferase, pas domain, cita, transmembrane signaling
Biological sourceGEOBACILLUS THERMODENITRIFICANS
Total number of polymer chains2
Total molecular weight25543.12
Authors
Schomburg, B.,Giller, K.,Becker, S. (deposition date: 2015-12-03, release date: 2017-01-11, modification date: 2017-03-01)
Primary citation
Weisenburger, S.,Boening, D.,Schomburg, B.,Giller, K.,Becker, S.,Griesinger, C.,Sandoghdar, V.
Cryogenic optical localization provides 3D protein structure data with Angstrom resolution.
Nat. Methods, 14:141-144, 2017
PubMed: 28068317
DOI: 10.1038/nmeth.4141
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.76 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.227702.3%0.9%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5fq1
no rotation
Molmil generated image of 5fq1
rotated about x axis by 90°
Molmil generated image of 5fq1
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BHISTIDINE KINASEpolymer11212444.92
UniProt (A4IPE6)
GEOBACILLUS THERMODENITRIFICANSCITA
GLYCEROLnon-polymer92.14
PHOSPHATE IONnon-polymer95.03
waterwater18.051

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight24889.8
Non-Polymers*Number of molecules7
Total molecular weight653.3
All*Total molecular weight25543.1
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.76 Å)

Cell axes34.45374.03675.081
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits37.54 - 1.76
the highest resolution shell value1.808 - 1.763
R-factor0.18645
R-work0.18501
the highest resolution shell value0.246
R-free0.21647
the highest resolution shell value0.274
RMSD bond length0.019
RMSD bond angle2.171

Data Collection Statistics

Resolution limits37.54 - 1.78
the highest resolution shell value -
Number of reflections18999
Rmerge_l_obs0.090
the highest resolution shell value0.510
Completeness99.3
Redundancy6.34
the highest resolution shell value6.14
I/sigma(I)2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
14.7

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC16BINDING SITE FOR RESIDUE GOL B 1309
ChainResidue
AGLU219
AHOH2008
BARG218
BGLU219
BARG307
BASN308

AC22BINDING SITE FOR RESIDUE GOL B 1310
ChainResidue
AARG218
AALA272

AC36BINDING SITE FOR RESIDUE GOL A 1309
ChainResidue
ASER199
AGLU201
AHIS260
AHOH2030
BLYS210
BGLN211

AC47BINDING SITE FOR RESIDUE GOL A 1310
ChainResidue
ALYS210
AGLN211
ATHR231
AMSE232
AVAL233
ALEU250
BHIS260

AC59BINDING SITE FOR RESIDUE PO4 A 1311
ChainResidue
ASER261
AARG262
ALEU263
AMSE278
AARG289
ASER304
APHE306
AHOH2018
AHOH2020

AC68BINDING SITE FOR RESIDUE PO4 B 1311
ChainResidue
BSER261
BARG262
BLEU263
BMSE278
BALA287
BARG289
BSER304
BPHE306

AC76BINDING SITE FOR RESIDUE PO4 A 1312
ChainResidue
AGLU202
AILE203
AGLY204
AASP276
AGLU277
AHOH2003

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
GOL_5fq1_A_13098GLYCEROL binding site
ChainResidueligand
ASER199-GLU201GOL: GLYCEROL
BTYR207GOL: GLYCEROL
BLYS210-GLN211GOL: GLYCEROL
BLEU214GOL: GLYCEROL
BTHR231GOL: GLYCEROL

GOL_5fq1_A_13108GLYCEROL binding site
ChainResidueligand
ALYS210-GLN211GOL: GLYCEROL
ALEU214GOL: GLYCEROL
ATHR231GOL: GLYCEROL
AVAL233GOL: GLYCEROL
AGLU246GOL: GLYCEROL
ALEU250GOL: GLYCEROL
BGLU209GOL: GLYCEROL

GOL_5fq1_B_13099GLYCEROL binding site
ChainResidueligand
AARG218-GLU219GOL: GLYCEROL
AARG307-ASN308GOL: GLYCEROL
BARG218-GLU219GOL: GLYCEROL
BPHE306-ASN308GOL: GLYCEROL

GOL_5fq1_B_13103GLYCEROL binding site
ChainResidueligand
AARG218GOL: GLYCEROL
BTYR274-ASP275GOL: GLYCEROL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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