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- PDB-1s3l: Structural and Functional Characterization of a Novel Archaeal Ph... -

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Basic information

Entry
Database: PDB / ID: 1s3l
TitleStructural and Functional Characterization of a Novel Archaeal Phosphodiesterase
ComponentsHypothetical protein MJ0936Hypothesis
KeywordsPHOSPHODIESTERASE / NUCLEASE / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / hydrolase activity / metal ion binding
Similarity search - Function
Phosphodiesterase YfcE, conserved site / Uncharacterized protein family UPF0025 signature. / YfcE-like, metallophosphatase domain / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like ...Phosphodiesterase YfcE, conserved site / Uncharacterized protein family UPF0025 signature. / YfcE-like, metallophosphatase domain / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphodiesterase MJ0936
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsChen, S. / Busso, D. / Yakunin, A.F. / Kuznetsova, E. / Proudfoot, M. / Jancrick, J. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural and functional characterization of a novel phosphodiesterase from Methanococcus jannaschii
Authors: Chen, S. / Yakunin, A.F. / Kuznetsova, E. / Busso, D. / Pufan, R. / Proudfoot, M. / Kim, R. / Kim, S.-H.
History
DepositionJan 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein MJ0936
B: Hypothetical protein MJ0936
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9325
Polymers43,8372
Non-polymers953
Water81145
1
A: Hypothetical protein MJ0936


Theoretical massNumber of molelcules
Total (without water)21,9192
Polymers21,9191
Non-polymers01
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Hypothetical protein MJ0936
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0143
Polymers21,9191
Non-polymers952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.722, 83.722, 149.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Hypothetical protein MJ0936 / Hypothesis


Mass: 21918.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: PSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3/PSJS1244 / References: UniProt: Q58346
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.7M AMMONIUM SULFATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.979
SYNCHROTRONALS 5.0.121
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDNov 21, 2002
ADSC QUANTUM 2102CCDNov 26, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
211
ReflectionResolution: 2.4→20 Å / Num. all: 20082 / Num. obs: 20082 / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 50.3 Å2 / Rsym value: 0.13 / Net I/σ(I): 24.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.37

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→46.41 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 789293.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1830 10 %RANDOM
Rwork0.226 ---
obs0.226 18238 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8502 Å2 / ksol: 0.358033 e/Å3
Displacement parametersBiso mean: 57.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.55 Å20 Å20 Å2
2--4.55 Å20 Å2
3----9.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 7 45 2711
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.682
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.232.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 240 9.6 %
Rwork0.279 2259 -
obs--75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMDNA-RNA.TOP

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