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- PDB-1v8p: Crystal structure of PAE2754 from Pyrobaculum aerophilum -

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Basic information

Entry
Database: PDB / ID: 1v8p
TitleCrystal structure of PAE2754 from Pyrobaculum aerophilum
Componentshypothetical protein PAE2754
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PIN-domain / tetramer
Function / homology
Function and homology information


exonuclease activity / RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
Pae0151-like, PIN domain / : / PIN domain / VapC family / 5'-nuclease / PIN domain / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.52 Å
AuthorsArcus, V.L. / Backbro, K. / Roos, A. / Daniel, E.L. / Baker, E.N.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease
Authors: Arcus, V.L. / Backbro, K. / Roos, A. / Daniel, E.L. / Baker, E.N.
History
DepositionJan 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein PAE2754
B: hypothetical protein PAE2754
C: hypothetical protein PAE2754
D: hypothetical protein PAE2754
E: hypothetical protein PAE2754
F: hypothetical protein PAE2754
G: hypothetical protein PAE2754
H: hypothetical protein PAE2754
I: hypothetical protein PAE2754
J: hypothetical protein PAE2754
K: hypothetical protein PAE2754
L: hypothetical protein PAE2754
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,29118
Polymers216,07812
Non-polymers2136
Water1,820101
1
A: hypothetical protein PAE2754
B: hypothetical protein PAE2754
C: hypothetical protein PAE2754
D: hypothetical protein PAE2754
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0976
Polymers72,0264
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-76 kcal/mol
Surface area22120 Å2
MethodPISA
2
E: hypothetical protein PAE2754
F: hypothetical protein PAE2754
G: hypothetical protein PAE2754
H: hypothetical protein PAE2754
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0976
Polymers72,0264
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-75 kcal/mol
Surface area22550 Å2
MethodPISA
3
I: hypothetical protein PAE2754
J: hypothetical protein PAE2754
K: hypothetical protein PAE2754
L: hypothetical protein PAE2754
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0976
Polymers72,0264
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-74 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.560, 165.190, 203.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer. There are three tetramers in the asymmetric unit.

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Components

#1: Protein
hypothetical protein PAE2754


Mass: 18006.518 Da / Num. of mol.: 12 / Mutation: P2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: PAE2754 / Plasmid: pPROEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZUJ3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.85 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: Tris-HCl, isopropanol, PEG 4000, trimethylamine-HCl, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Arcus, V.L., (2004) Acta Cryst., D60, 733.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
250 mMTris-HCl1droppH9.2
350 mM1dropNaCl
4100 mMTris-HCl1reservoirpH9.2
530 %2-propanol1reservoir
618 %PEG40001reservoir
710 mMtrimethylamine-HCl1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2002
RadiationMonochromator: collimating mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 69531 / Num. obs: 69531 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.2 / Num. unique all: 6245 / % possible all: 91.4
Reflection
*PLUS
Num. measured all: 879180
Reflection shell
*PLUS
% possible obs: 91.4 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.52→49.63 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2765571.25 / 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
Rfree0.305 3406 5 %RANDOM
Rwork0.25 ---
all0.253 71103 --
obs0.25 67697 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.8894 Å2 / ksol: 0.337859 e/Å3
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1-3.07 Å20 Å20 Å2
2--4.53 Å20 Å2
3----7.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.52→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12657 0 6 101 12764
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scbond_it1.512
X-RAY DIFFRACTIONc_scangle_it2.32.5
LS refinement shellResolution: 2.52→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 407 4.6 %
Rwork0.335 8412 -
obs-6245 75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Highest resolution: 2.5 Å

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