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- PDB-1xsq: Crystal structure of ureidoglycolate hydrolase from E.coli. North... -

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Basic information

Entry
Database: PDB / ID: 1xsq
TitleCrystal structure of ureidoglycolate hydrolase from E.coli. Northeast Structural Genomics Consortium target ET81.
ComponentsUreidoglycolate hydrolase
KeywordsHYDROLASE / Northeast Structural Genomics Consortium / NESG / Structural Genomics / Protein Structure Initiative / PSI / ET81
Function / homology
Function and homology information


ureidoglycolate lyase / ureidoglycolate lyase activity / ureidoglycolate hydrolase activity / allantoin catabolic process / purine nucleobase catabolic process
Similarity search - Function
Ureidoglycolate hydrolase / Ureidoglycolate lyase / Ureidoglycolate lyase, bacterial / Ureidoglycolate lyase domain superfamily / Ureidoglycolate lyase / RmlC-like cupin domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ureidoglycolate lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsKuzin, A.P. / Vorobiev, S.M. / Abashidze, M. / Acton, T.B. / Ma, L.-C. / Xiao, R. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of ureidoglycolate hydrolase from E.coli. Northeast Structural Genomics Consortium target ET81.
Authors: Kuzin, A.P. / Vorobiev, S.M. / Abashidze, M. / Acton, T.B. / Ma, L.-C. / Xiao, R. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionOct 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ureidoglycolate hydrolase
B: Ureidoglycolate hydrolase


Theoretical massNumber of molelcules
Total (without water)38,7052
Polymers38,7052
Non-polymers00
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-19 kcal/mol
Surface area14850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.194, 45.273, 51.801
Angle α, β, γ (deg.)100.70, 99.84, 117.19
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ureidoglycolate hydrolase


Mass: 19352.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: allA / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)+Magic / References: UniProt: P77731, EC: 3.5.3.19
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na-citrate, Na-formate, PEG-3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 5, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 80698 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 42.7
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 5.9 / % possible all: 77.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.6→24.34 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 711546.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3524 4.8 %RANDOM
Rwork0.227 ---
obs0.227 73679 85 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6812 Å2 / ksol: 0.369831 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.533 Å2-0.893 Å20.78 Å2
2--5.625 Å21.708 Å2
3---4.091 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.6→24.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 0 246 2742
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.3831.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it2.1152
X-RAY DIFFRACTIONc_scangle_it3.1482.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 425 4.8 %
Rwork0.227 8469 -
obs--61.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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