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- PDB-2h0j: Crystal structure of PucM in the presence of 5,6-diaminouracil -

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Basic information

Entry
Database: PDB / ID: 2h0j
TitleCrystal structure of PucM in the presence of 5,6-diaminouracil
ComponentsTransthyretin-like protein pucM
KeywordsHYDROLASE / BETA SANDWITCH / COMPLEX WITH DIAMINOURACIL / HIU
Function / homology
Function and homology information


hydroxyisourate hydrolase / hydroxyisourate hydrolase activity / urate catabolic process / purine nucleobase metabolic process / identical protein binding
Similarity search - Function
Hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family ...Hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
5,6-DIAMINOPYRIMIDINE-2,4(1H,3H)-DIONE / 5-hydroxyisourate hydrolase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsRhee, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural and functional analysis of PucM, a hydrolase in the ureide pathway and a member of the transthyretin-related protein family.
Authors: Jung, D.-K. / Lee, Y. / Park, S.G. / Park, B.C. / Kim, G.-H. / Rhee, S.
History
DepositionMay 15, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transthyretin-like protein pucM
B: Transthyretin-like protein pucM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5503
Polymers27,4072
Non-polymers1421
Water1,00956
1
A: Transthyretin-like protein pucM
hetero molecules

A: Transthyretin-like protein pucM
hetero molecules

A: Transthyretin-like protein pucM
hetero molecules

A: Transthyretin-like protein pucM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3838
Polymers54,8154
Non-polymers5684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation7_465y-1,x+1,-z+1/21
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
2
B: Transthyretin-like protein pucM

B: Transthyretin-like protein pucM

B: Transthyretin-like protein pucM

B: Transthyretin-like protein pucM


Theoretical massNumber of molelcules
Total (without water)54,8154
Polymers54,8154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)72.956, 72.956, 145.127
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

21B-302-

HOH

DetailsChain A and B forms independently a homotetramer by a crystallographic symmetry-related molecules

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Components

#1: Protein Transthyretin-like protein pucM


Mass: 13703.716 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32142
#2: Chemical ChemComp-URN / 5,6-DIAMINOPYRIMIDINE-2,4(1H,3H)-DIONE / 5,6-DIAMINOURACIL


Mass: 142.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.2
Details: 0.1M ammonium acetate, 0.5M NaCl, 0.5M ammonium sulfate, pH 4.2, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97144 Å
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Oct 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97144 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 9261 / Num. obs: 9261 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.107 / Χ2: 0.823 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-370.5468880.666100
3-3.126.90.3729170.701100
3.12-3.276.90.2978850.771100
3.27-3.446.90.1869090.797100
3.44-3.656.80.1449030.88100
3.65-3.936.80.129050.902100
3.93-4.336.70.0889290.867100
4.33-4.956.60.069370.962100
4.95-6.236.40.069520.807100
6.23-305.70.04110360.88299.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.9→30 Å / σ(F): 991 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 774 8.4 %RANDOM
Rwork0.211 ---
obs0.211 7765 84 %-
all-7765 --
Solvent computationBsol: 20.282 Å2
Displacement parametersBiso mean: 38.66 Å2
Baniso -1Baniso -2Baniso -3
1--3.611 Å20 Å20 Å2
2---3.611 Å20 Å2
3---7.222 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 10 56 1836
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.6981.5
X-RAY DIFFRACTIONc_scbond_it2.442
X-RAY DIFFRACTIONc_mcangle_it3.072
X-RAY DIFFRACTIONc_scangle_it3.6722.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dau.param
X-RAY DIFFRACTION3water_rep.param

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