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- PDB-1k2e: crystal structure of a nudix protein from Pyrobaculum aerophilum -

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Basic information

Entry
Database: PDB / ID: 1k2e
Titlecrystal structure of a nudix protein from Pyrobaculum aerophilum
ComponentsNUDIX HOMOLOG
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Nudix/MutT-like fold / Mixed alpha/beta / dimer / putative Nudix hydrolase
Function / homology
Function and homology information


NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / NICKEL (II) ION / MutT/nudix family protein
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionSep 26, 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: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: NUDIX HOMOLOG
B: NUDIX HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,60914
Polymers35,6272
Non-polymers98212
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-76 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.712, 72.612, 85.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer as in the asymmetric unit.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NUDIX HOMOLOG


Mass: 17813.570 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 255 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG 4000, ammonium sulfate, sodium acetate, isopropanol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris1drop
25 mMEDTA1droppH8.0
310.0 mg/mlprotein1drop
45-8 %PEG40001reservoiror PEG2000MME
55 %2-propanol1reservoir
650 mMammonium sulfate1reservoir
7100 mM1reservoirpH4.8NaOAc

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 12, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 30654 / Num. obs: 30654 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 14.6 Å2 / Rsym value: 0.08 / Net I/σ(I): 18.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.36 % / Mean I/σ(I) obs: 3.26 / Num. unique all: 2934 / Rsym value: 0.443 / % possible all: 96.4
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 398012 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 96.4 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K26, same protein solved by SAD with iridium derivative data.

1k26


Resolution: 1.8→19.74 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1466528.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2463 8.1 %RANDOM
Rwork0.184 ---
all-30585 --
obs-30585 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.1588 Å2 / ksol: 0.38221 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.46 Å20 Å20 Å2
2---0.32 Å20 Å2
3---3.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 56 243 2713
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.841.5
X-RAY DIFFRACTIONc_mcangle_it2.562
X-RAY DIFFRACTIONc_scbond_it3.142
X-RAY DIFFRACTIONc_scangle_it4.482.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 393 8.1 %
Rwork0.234 4457 -
obs-4838 95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4OTHERS.PAROTHERS.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 8 % / Rfactor obs: 0.183 / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09
LS refinement shell
*PLUS
Rfactor Rfree: 0.289 / Rfactor Rwork: 0.234

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