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- PDB-3qva: Structure of Klebsiella pneumoniae 5-hydroxyisourate hydrolase -

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Basic information

Entry
Database: PDB / ID: 3qva
TitleStructure of Klebsiella pneumoniae 5-hydroxyisourate hydrolase
ComponentsTransthyretin-like protein
KeywordsHYDROLASE / Transthyretin-related protein / 5-hydroxyisourate hydrolase
Function / homology
Function and homology information


hydroxyisourate hydrolase / hydroxyisourate hydrolase activity / purine nucleobase metabolic process
Similarity search - Function
Hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / 5-hydroxyisourate hydrolase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.755 Å
AuthorsFrench, J.B. / Ealick, S.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural and kinetic insights into the mechanism of 5-hydroxyisourate hydrolase from Klebsiella pneumoniae.
Authors: French, J.B. / Ealick, S.E.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Assembly

Deposited unit
A: Transthyretin-like protein
B: Transthyretin-like protein
C: Transthyretin-like protein
D: Transthyretin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9576
Polymers49,7674
Non-polymers1902
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-49 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.192, 101.302, 106.111
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Transthyretin-like protein


Mass: 12441.810 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: HpxT, KPN78578_16360, KPN_01666 / Plasmid: Pet28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A6T926
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M imidazole pH 7.5-8.5, 0.5 - 1.0 M ammonium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2009
RadiationMonochromator: focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.755→73.272 Å / Num. all: 45752 / Num. obs: 45752 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.044 / Χ2: 1.229 / Net I/σ(I): 18.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.755-1.824.80.12845050.9491100
1.82-1.94.90.09345320.9151100
1.9-1.984.90.07145170.962199.9
1.98-2.094.90.0645551.0951100
2.09-2.224.90.05245671.207199.9
2.22-2.394.90.04745621.268199.9
2.39-2.634.90.04245941.291199.9
2.63-3.014.80.04246191.674199.8
3.01-3.794.80.04946611.444199.8
3.79-504.40.0346401.497195

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.755→73.27 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.122 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 2304 5.1 %RANDOM
Rwork0.1986 ---
all0.1998 45752 --
obs0.1998 45556 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.18 Å2 / Biso mean: 18.8049 Å2 / Biso min: 8.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.51 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.755→73.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3109 0 10 303 3422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213223
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9414403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3615421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70620.667120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20915433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5091529
X-RAY DIFFRACTIONr_chiral_restr0.0830.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212448
X-RAY DIFFRACTIONr_mcbond_it0.6431.52091
X-RAY DIFFRACTIONr_mcangle_it1.23123327
X-RAY DIFFRACTIONr_scbond_it1.50631132
X-RAY DIFFRACTIONr_scangle_it2.4814.51072
LS refinement shellResolution: 1.755→1.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 160 -
Rwork0.259 2965 -
all-3125 -
obs--93.37 %

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