1DKU

CRYSTAL STRUCTURES OF BACILLUS SUBTILIS PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE: MOLECULAR BASIS OF ALLOSTERIC INHIBITION AND ACTIVATION.

> Summary

Summary for 1DKU

Related1DKR
DescriptorPHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE (E.C.2.7.6.1)
Functional Keywordsopen alpha-beta structure, domain duplication, phosphoribosyltransferase type i fold, transferase
Biological sourceBacillus subtilis
Cellular locationCytoplasm (By similarity) P14193
Total number of polymer chains2
Total molecular weight71361.95
Authors
Eriksen, T.A.,Kadziola, A.,Bentsen, A.-K.,Harlow, K.W.,Larsen, S. (deposition date: 1999-12-08, release date: 2000-04-05, modification date: 2009-02-24)
Primary citation
Eriksen, T.A.,Kadziola, A.,Bentsen, A.K.,Harlow, K.W.,Larsen, S.
Structural basis for the function of Bacillus subtilis phosphoribosyl-pyrophosphate synthetase.
Nat.Struct.Biol., 7:303-308, 2000
PubMed: 10742175
DOI: 10.1038/74069
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.2 Å)
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Structure validation

ClashscoreRamachandran outliersSidechain outliersRSRZ outliers804.4%0.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BPROTEIN (PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE)polymer31734910.52
UniProt (P14193)
Pfam (PF13793)
Pfam (PF14572)
Bacillus subtilis@PDBjRIBOSE-PHOSPHATE PYROPHOSPHOKINASE
PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTERnon-polymer425.22
METHYL PHOSPHONIC ACID ADENOSINE ESTERnon-polymer345.32
waterwater18.0180

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight69821.0
Non-Polymers*Number of molecules4
Total molecular weight1541.0
All*Total molecular weight71361.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.2 Å)
Cell axes115.650115.650106.410
Cell angles90.0090.00120.00
SpacegroupP 63
Resolution limits30.00 - 2.20
the highest resolution shell value -
R-factor0.198
R-work0.19800
R-free0.24100
RMSD bond length0.016
RMSD bond angle2.011*

Data Collection Statistics

Resolution limits23.00 - 1.70 (2.20*)
the highest resolution shell value2.35* - 2.20*
Number of reflections83506 (40252*)
Rmerge_l_obs0.129 (0.067*)
the highest resolution shell value0.037 (0.265*)
Completeness97.3 (98.6*)
the highest resolution shell value98.8*
Redundancy3.1
the highest resolution shell value2.7
I/sigma(I)0 (0.0*)

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP8293unknown*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropprotein7 (mg/ml)
21dropmADP25 (mM)
31drop50 (mM)
41dropbeta-octylglucoside0.5 (%(w/v))
51reservoirsodium citrate1 (M)
61reservoirHEPES0.1 (M)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0005524molecular_functionATP binding
A0016301molecular_functionkinase activity
A0000287molecular_functionmagnesium ion binding
A0004749molecular_functionribose phosphate diphosphokinase activity
A0006015biological_process5-phosphoribose 1-diphosphate biosynthetic process
A0009165biological_processnucleotide biosynthetic process
A0009156biological_processribonucleoside monophosphate biosynthetic process
B0005737cellular_componentcytoplasm
B0005524molecular_functionATP binding
B0016301molecular_functionkinase activity
B0000287molecular_functionmagnesium ion binding
B0004749molecular_functionribose phosphate diphosphokinase activity
B0006015biological_process5-phosphoribose 1-diphosphate biosynthetic process
B0009165biological_processnucleotide biosynthetic process
B0009156biological_processribonucleoside monophosphate biosynthetic process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC115BINDING SITE FOR RESIDUE AP2 B 1001
ChainResidue
ALYS106
ASER109
AARG110
BSER53
BARG55
BGLN141
BASP149
BHIS150
BSER311
BVAL312
BSER313
BPHE316
BHOH
BHOH
BHOH

AC216BINDING SITE FOR RESIDUE AP2 A 1002
ChainResidue
ASER53
AARG55
AGLN141
AASP149
AHIS150
ASER311
AVAL312
ASER313
APHE316
AHOH
BLYS106
BALA107
BARG108
BSER109
BARG110
BHOH

AC311BINDING SITE FOR RESIDUE ABM A 1003
ChainResidue
AARG102
AGLN103
AALA107
AHIS136
AHOH
AHOH
AHOH
AHOH
BPHE41
BASP43
BGLU45

AC410BINDING SITE FOR RESIDUE ABM B 1004
ChainResidue
APHE41
AASP43
AGLU45
BARG102
BGLN103
BARG105
BALA107
BGLU111
BHIS136
BHOH

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

site_idNumber of ResiduesDetails
ABM_1dku_A_10039METHYL PHOSPHONIC ACID ADENOSINE ESTER binding site
ChainResidueligand
AARG101-ARG104ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER
AALA106ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER
AGLU110ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER
AHIS135ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER
AASP174ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER
AASP227ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER

AP2_1dku_B_100117PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER binding site
ChainResidueligand
ALYS105-GLU110AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
BGLN140AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
BILE147-MET151AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
BGLN309-SER312AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
BPHE315AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

AP2_1dku_A_100217PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER binding site
ChainResidueligand
AGLN140AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
AILE147-HIS149AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
AMET151AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
AGLN309-TYR313AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
APHE315AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
BLYS105-GLU110AP2: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER

ABM_1dku_B_10048METHYL PHOSPHONIC ACID ADENOSINE ESTER binding site
ChainResidueligand
BARG101-GLN102ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER
BARG104ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER
BALA106ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER
BGLU110ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER
BHIS135ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER
BASP174ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER
BASP227ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS001032Purine/pyrimidine phosphoribosyl transferases signature. [LIVMFYWCTA]-[LIVM]-[LIVMA]-[LIVMFC]-[DE]-D-[LIVMS]-[LIVM]-[STAVD]
ChainResidueDetails
ANA*
BNA*

PS001142Phosphoribosyl pyrophosphate synthase signature. D-[LIM]-H-[SANDT]-x-[QS]-[IMSTAVF]-[QMLPH]-[GA]-[FY]-F-x(2)-P
ChainResidueDetails
ANA*
BNA*

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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
CSA14Annotated By Reference To The Literature 1a95
ChainResidueDetails
AASP224
AASP223
AASP227
ACYS250

CSA24Annotated By Reference To The Literature 1a95
ChainResidueDetails
BASP224
BASP223
BASP227
BCYS250

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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb1dku.ent.gz (103.41 KB)
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all (no-compress)pdb1dku.ent (434.98 KB)
header onlypdb1dku.ent.gz (7.2 KB)
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PDBx/mmCIF1dku.cif.gz (127.42 KB)
PDBMLall1dku.xml.gz (194.91 KB)
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no-atom1dku-noatom.xml.gz (28.99 KB)
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ext-atom1dku-extatom.xml.gz (112.8 KB)
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PDBMLplusall1dku-plus.xml.gz (198.45 KB)
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no-atom1dku-plus-noatom.xml.gz (32.52 KB)
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add only1dku-add.xml.gz (3.54 KB)
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RDF1dku.rdf.gz (61.44 KB)
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Structure factorsr1dkusf.ent.gz (465.54 KB)
Biological unit (PDB format)1dku.pdb1.gz (98.53 KB) (A,B)
*author and software defined assembly, 2 molecule(s) (dimeric)
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1dku.pdb2.gz (288.8 KB) (A,B)
*software defined assembly, 6 molecule(s) (hexameric)
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1dku.pdb3.gz (98.88 KB) (A)
*software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF1dku​_validation.pdf.gz (295.48 KB)
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PDF-full1dku​_full​_validation.pdf.gz (306.01 KB)
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XML1dku​_validation.xml.gz (27.29 KB)
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PNG1dku​_multipercentile​_validation.png.gz (139 KB)
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SVG1dku​_multipercentile​_validation.svg.gz (862 B)
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Sequence (fasta)1dku​_seq.txt
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