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- PDB-1s3n: Structural and Functional Characterization of a Novel Archaeal Ph... -

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Basic information

Entry
Database: PDB / ID: 1s3n
TitleStructural and Functional Characterization of a Novel Archaeal Phosphodiesterase
ComponentsHypothetical protein MJ0936
KeywordsPHOSPHODIESTERASE / PHOSPHODIESTERASE/NUCLEASE / DI-METAL-BINDING / 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 ...: / 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
: / Phosphodiesterase MJ0936
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_asym_id / _struct_conn.ptnr2_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,0576
Polymers43,8372
Non-polymers2204
Water1,08160
1
A: Hypothetical protein MJ0936
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0283
Polymers21,9191
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein MJ0936
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0283
Polymers21,9191
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Hypothetical protein MJ0936
B: Hypothetical protein MJ0936
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)88,11412
Polymers87,6744
Non-polymers4408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-y+1,z1
Buried area6070 Å2
ΔGint-90 kcal/mol
Surface area25400 Å2
MethodPISA
4
A: Hypothetical protein MJ0936
hetero molecules

A: Hypothetical protein MJ0936
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0576
Polymers43,8372
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-y+1,z1
MethodPQS
5
B: Hypothetical protein MJ0936
hetero molecules

B: Hypothetical protein MJ0936
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0576
Polymers43,8372
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.398, 70.398, 196.705
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


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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.7M AMMONIUM SULFATE, 5mM manganese sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 16434 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.05

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35.2 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 306193.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1470 9.9 %RANDOM
Rwork0.22 ---
obs0.22 14802 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.4124 Å2 / ksol: 0.326675 e/Å3
Displacement parametersBiso mean: 61 Å2
Baniso -1Baniso -2Baniso -3
1-9.52 Å20 Å20 Å2
2--9.52 Å20 Å2
3----19.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 4 60 2724
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.671.5
X-RAY DIFFRACTIONc_mcangle_it2.942
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.792.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 191 9.6 %
Rwork0.297 1801 -
obs--73.1 %
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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