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- PDB-1v8o: Crystal Structure of PAE2754 from Pyrobaculum aerophilum -

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Basic information

Entry
Database: PDB / ID: 1v8o
TitleCrystal Structure of PAE2754 from Pyrobaculum aerophilum
Componentshypothetical protein PAE2754
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PIN-domain / SeMet substituted
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 with data collection on Se-Met crystal at 0.97941 A / Resolution: 2.8 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 1.3Mar 14, 2018Group: Advisory / Database references / Category: pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,60812
Polymers145,4668
Non-polymers1424
Water1,18966
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)72,8046
Polymers72,7334
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-79 kcal/mol
Surface area22790 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)72,8046
Polymers72,7334
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-79 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.360, 192.780, 60.440
Angle α, β, γ (deg.)90.00, 94.68, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a tetramer. There are two tetramers in the asymmetric unit.

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Components

#1: Protein
hypothetical protein PAE2754


Mass: 18183.279 Da / Num. of mol.: 8 / Mutation: P2A, L65M, L80M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: PAE2754 / Plasmid: pPROEX / Production host: Escherichia coli (E. coli) / Strain (production host): DL41(DE3) / References: UniProt: Q8ZUJ3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.75 Å3/Da / Density % sol: 54.96 %
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
15-10 mg/mlprotein1drop
250 mMTris-HCl1droppH9.2
350 mM1dropNaCl
4100 mMTris-HCl1reservoirpH9.2
525-30 %2-propanol1reservoir
617-20 %PEG40001reservoir
710 mMtrimethylamine-HCl1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97941, 0.83208
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 26, 2003
RadiationMonochromator: Curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979411
20.832081
ReflectionResolution: 2.75→40 Å / Num. all: 62023 / Num. obs: 32550 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.7
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2444 / % possible all: 72.7
Reflection
*PLUS
Num. measured all: 286429
Reflection shell
*PLUS
% possible obs: 72.7 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD with data collection on Se-Met crystal at 0.97941 A
Resolution: 2.8→36.58 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1623333.4 / 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
Rfree0.279 2853 4.8 %RANDOM
Rwork0.226 ---
all0.229 32550 --
obs0.226 32550 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.6186 Å2 / ksol: 0.34703 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å20 Å23.06 Å2
2---2.93 Å20 Å2
3----0.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.8→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8424 0 4 66 8494
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_d20.3
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it6.191.5
X-RAY DIFFRACTIONc_mcangle_it9.612
X-RAY DIFFRACTIONc_scbond_it8.972
X-RAY DIFFRACTIONc_scangle_it12.642.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 392 4.8 %
Rwork0.327 7753 -
obs-7753 78.1 %
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: 2.8 Å / Lowest resolution: 40 Å
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_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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