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- PDB-2pe3: Crystal structure of Frv operon protein FRVX (PH1821)from pyrococ... -

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Basic information

Entry
Database: PDB / ID: 2pe3
TitleCrystal structure of Frv operon protein FRVX (PH1821)from pyrococcus horikoshii OT3
Components354aa long hypothetical operon protein Frv
KeywordsHYDROLASE / Aminopeptidase / self-compartmentalizing / metalloprotease / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


aminopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
: / Peptidase M42, domain 2 / Peptidase M42, domain 2 / : / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel ...: / Peptidase M42, domain 2 / Peptidase M42, domain 2 / : / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
354aa long hypothetical operon protein Frv
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJeyakanthan, J. / Kanaujia, S.P. / Rafi, Z.A. / Sekar, K. / Inagakai, E. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of frv operon protein frvx (ph1821)from pyrococcus horikoshii OT3
Authors: Jeyakanthan, J. / Kanaujia, S.P. / Rafi, Z.A. / Sekar, K. / Inagaki, E. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S.
History
DepositionApr 2, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 354aa long hypothetical operon protein Frv
B: 354aa long hypothetical operon protein Frv
C: 354aa long hypothetical operon protein Frv
D: 354aa long hypothetical operon protein Frv


Theoretical massNumber of molelcules
Total (without water)156,2354
Polymers156,2354
Non-polymers00
Water10,719595
1
A: 354aa long hypothetical operon protein Frv
B: 354aa long hypothetical operon protein Frv
C: 354aa long hypothetical operon protein Frv
D: 354aa long hypothetical operon protein Frv

A: 354aa long hypothetical operon protein Frv
B: 354aa long hypothetical operon protein Frv
C: 354aa long hypothetical operon protein Frv
D: 354aa long hypothetical operon protein Frv

A: 354aa long hypothetical operon protein Frv
B: 354aa long hypothetical operon protein Frv
C: 354aa long hypothetical operon protein Frv
D: 354aa long hypothetical operon protein Frv


Theoretical massNumber of molelcules
Total (without water)468,70512
Polymers468,70512
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area46640 Å2
ΔGint-249 kcal/mol
Surface area121400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.608, 125.608, 277.323
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
354aa long hypothetical operon protein Frv / Frv operon protein FRVX


Mass: 39058.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 CONDON PLUS (DE3)-RIL / References: UniProt: O59485
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 7% PEG 6K, 1M NaCl, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 19, 2004 / Details: RH COATED BENT-CYRINDRICAL MIRROR
RadiationMonochromator: SI-1 1 1 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 107669 / % possible obs: 97.5 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.054
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.477 / Num. unique all: 10649 / Rsym value: 0.415 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XFO

1xfo


Resolution: 2→40.67 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 11980599.04 / 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
Rfree0.197 1912 1.8 %RANDOM
Rwork0.166 ---
obs0.166 105428 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.1226 Å2 / ksol: 0.331803 e/Å3
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.99 Å24.15 Å20 Å2
2--3.99 Å20 Å2
3----7.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2→40.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10209 0 0 595 10804
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.611.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.482.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.322 224 -
Rwork0.319 --
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION5water_rep.paramwater_protin.top

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