1A0A

PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX

> Summary

Summary for 1A0A

DescriptorPHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX
Functional Keywordstranscription factor, basic helix loop helix, complex (transcription factor-dna), transcription-dna complex, transcription/dna
Biological sourceSaccharomyces cerevisiae (baker's yeast)
Cellular locationCytoplasm P07270
Total number of polymer chains4
Total molecular weight24624.1
Authors
Shimizu, T.,Toumoto, A.,Ihara, K.,Shimizu, M.,Kyogoku, Y.,Ogawa, N.,Oshima, Y.,Hakoshima, T. (deposition date: 1997-11-27, release date: 1998-03-18, modification date: 2009-02-24)
Primary citation
Shimizu, T.,Toumoto, A.,Ihara, K.,Shimizu, M.,Kyogoku, Y.,Ogawa, N.,Oshima, Y.,Hakoshima, T.
Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition.
EMBO J., 16:4689-4697, 1997
PubMed: 9303313
DOI: 10.1093/emboj/16.15.4689
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.8 Å)
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Structure validation

ClashscoreRamachandran outliersSidechain outliers14817.2%31.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1a0a
no rotation
Molmil generated image of 1a0a
rotated about x axis by 90°
Molmil generated image of 1a0a
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
CDNA (5'-D(*CP*TP*CP*AP*CP*AP*CP*GP*TP*GP*GP*GP*AP*CP*TP*AP*G )-3')polymer175212.41
UASP2(17)
DDNA (5'-D(*CP*TP*AP*GP*TP*CP*CP*CP*AP*CP*GP*TP*GP*TP*GP*AP*G )-3')polymer175203.41
UASP2(17)
A, BPROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4)polymer637104.12
UniProt (P07270)
Pfam (PF00010)
Saccharomyces cerevisiae (baker's yeast)@PDBjBHLH
waterwater18.080

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight24624.1
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight24624.1
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.8 Å)
Cell axes53.51068.300108.770
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits8.00 - 2.80
the highest resolution shell value2.920 - 2.800
R-factor0.230*
R-work0.23000
the highest resolution shell value0.257
R-free0.28400
the highest resolution shell value0.319
RMSD bond length0.011
RMSD bond angle2.420 (23.900*)

Data Collection Statistics

Resolution limits - 2.80
the highest resolution shell value2.95* - 2.80*
Number of reflections9398
Number of measurements36943*
Rmerge_l_obs0.087
the highest resolution shell value0.202
Completeness92.0
the highest resolution shell value76.8*
Redundancy3.9
the highest resolution shell value1.9
I/sigma(I)1 (1.0*)

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1vapor diffusion3.6unknown*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
111PEG 6000
211NA CITRATE
312PEG 6000
412NA CITRATE
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropprotein0.4 (mM)
21dropDNA0.2 (mM)
31dropPEG60001 (%(w/v))
41dropsodium citrate20 (mM)
51reservoirPEG60001 (%(w/v))
61reservoirsodium citrate20 (mM)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0005634cellular_componentnucleus
A0043565molecular_functionsequence-specific DNA binding
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0016036biological_processcellular response to phosphate starvation
A0006338biological_processchromatin remodeling
A0045937biological_processpositive regulation of phosphate metabolic process
A0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
A0006351biological_processtranscription, DNA-templated
B0005737cellular_componentcytoplasm
B0005634cellular_componentnucleus
B0043565molecular_functionsequence-specific DNA binding
B0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
B0016036biological_processcellular response to phosphate starvation
B0006338biological_processchromatin remodeling
B0045937biological_processpositive regulation of phosphate metabolic process
B0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
B0006351biological_processtranscription, DNA-templated
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Functional Information from PDB Data

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

site_idNumber of ResiduesDetails
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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
SWS_FT_FI11Basic motif.
ChainResidueDetails
ANA*

SWS_FT_FI21Basic motif.
ChainResidueDetails
BNA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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