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- PDB-1jrk: Crystal Structure of a Nudix Protein from Pyrobaculum aerophilum ... -

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Basic information

Entry
Database: PDB / ID: 1jrk
TitleCrystal Structure of a Nudix Protein from Pyrobaculum aerophilum Reveals a Dimer with Intertwined Beta Sheets
ComponentsNudix homolog
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Nudix/mutT-like fold / mixed alpha/beta / tetramerization due to Hix6x tag / putative Nudix hydrolase
Function / homology
Function and homology information


Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
MutT/nudix family protein
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, S. / Mura, C. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit beta-sheets.
Authors: Wang, S. / Mura, C. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
History
DepositionAug 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). The putative biologically-relevant assembly is a dimer, and two of these associate to form a weak tetramer in the asymmetric unit. Chains A+B and C+D form the two dimers.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nudix homolog
B: Nudix homolog
C: Nudix homolog
D: Nudix homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,96310
Polymers71,2544
Non-polymers7096
Water3,117173
1
A: Nudix homolog
B: Nudix homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9825
Polymers35,6272
Non-polymers3553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-58 kcal/mol
Surface area14660 Å2
MethodPISA
2
C: Nudix homolog
D: Nudix homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9825
Polymers35,6272
Non-polymers3553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-60 kcal/mol
Surface area14970 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-150 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.469, 81.464, 73.888
Angle α, β, γ (deg.)90.00, 99.96, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe putative biologically-relevant assembly is a dimer, and two of these associate to form a tetramer in the asymmetric unit. Chains A+B and C+D form the two dimers.

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Components

#1: Protein
Nudix homolog


Mass: 17813.570 Da / Num. of mol.: 4 / Mutation: M16L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Plasmid: PET-22B_MUTT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZTD8
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Tris, MPD, MES buffer, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris1drop
25 mMEDTA1droppH8.0
310.0 mg/mlprotein1drop
4100 mMMES1reservoirpH6.2
515 %MPD1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 21, 2001 / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→90 Å / Num. all: 23707 / Num. obs: 23707 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.1
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3 / Num. unique all: 2324 / % possible all: 97
Reflection
*PLUS
Lowest resolution: 90 Å / Num. measured all: 84048 / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.465

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P. aerophilum mutT dimer solved in another space group (P21) by Wang et al.

Resolution: 2.4→20 Å
Isotropic thermal model: restrained isotropic temperature factors
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1103 4.8 %random
Rwork0.19 ---
all-22891 --
obs-22891 95.2 %-
Displacement parametersBiso mean: 33.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4728 0 0 221 4949
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.757
X-RAY DIFFRACTIONc_dihedral_angle_d24.61
X-RAY DIFFRACTIONc_improper_angle_d1.038
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.346 --
Rwork0.247 --
obs-3416 89.4 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 8 % / Rfactor obs: 0.19 / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.61
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.038
LS refinement shell
*PLUS
Rfactor Rfree: 0.346 / Rfactor Rwork: 0.247

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