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- PDB-2ahd: The Apo structure of Methanococcus jannaschii phosphodiesterase MJ0936 -

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Basic information

Entry
Database: PDB / ID: 2ahd
TitleThe Apo structure of Methanococcus jannaschii phosphodiesterase MJ0936
ComponentsPhosphodiesterase MJ0936
KeywordsHYDROLASE / phosphodiesterase / Structural Genomics / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
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: 3 Å
AuthorsChen, S. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: TO BE PUBLISHED
Title: The Apo structure of Methanococcus jannaschii phosphodiesterase MJ0936
Authors: Chen, S. / Kim, R. / Kim, S.-H.
History
DepositionJul 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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: Phosphodiesterase MJ0936
B: Phosphodiesterase MJ0936
C: Phosphodiesterase MJ0936
D: Phosphodiesterase MJ0936


Theoretical massNumber of molelcules
Total (without water)75,7264
Polymers75,7264
Non-polymers00
Water2,684149
1
A: Phosphodiesterase MJ0936


Theoretical massNumber of molelcules
Total (without water)18,9311
Polymers18,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Phosphodiesterase MJ0936


Theoretical massNumber of molelcules
Total (without water)18,9311
Polymers18,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Phosphodiesterase MJ0936


Theoretical massNumber of molelcules
Total (without water)18,9311
Polymers18,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Phosphodiesterase MJ0936


Theoretical massNumber of molelcules
Total (without water)18,9311
Polymers18,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
A: Phosphodiesterase MJ0936
B: Phosphodiesterase MJ0936

C: Phosphodiesterase MJ0936
D: Phosphodiesterase MJ0936


Theoretical massNumber of molelcules
Total (without water)75,7264
Polymers75,7264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area4830 Å2
ΔGint-49 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.866, 71.342, 62.969
Angle α, β, γ (deg.)90.00, 98.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Phosphodiesterase MJ0936


Mass: 18931.451 Da / Num. of mol.: 4
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, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 0.2 M sodium acetate, 30% PEG 4000, 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: Nov 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 18648 / Num. obs: 17430 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1S3M

1s3m


Resolution: 3→44.78 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 272853.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1701 9.8 %RANDOM
Rwork0.235 ---
obs0.235 17430 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.7722 Å2 / ksol: 0.338479 e/Å3
Displacement parametersBiso mean: 78.2 Å2
Baniso -1Baniso -2Baniso -3
1--28.44 Å20 Å2-11.48 Å2
2--2.21 Å20 Å2
3---26.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 3→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5320 0 0 149 5469
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.453 229 9.1 %
Rwork0.367 2296 -
obs--82.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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