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- PDB-2xmo: The crystal structure of Lmo2642 -

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Basic information

Entry
Database: PDB / ID: 2xmo
TitleThe crystal structure of Lmo2642
ComponentsLMO2642 PROTEIN
KeywordsHYDROLASE / PHOSPHODIESTERASE
Function / homology
Function and homology information


Serum Albumin; Chain A, Domain 1 - #180 / Phosphoesterase, lmo2642-related / Cyclic nucleotide phosphodiesterase, C-terminal domain / C-terminal domain of cyclic nucleotide phosphodiesterase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Serum Albumin; Chain A, Domain 1 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like ...Serum Albumin; Chain A, Domain 1 - #180 / Phosphoesterase, lmo2642-related / Cyclic nucleotide phosphodiesterase, C-terminal domain / C-terminal domain of cyclic nucleotide phosphodiesterase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Serum Albumin; Chain A, Domain 1 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / : / PHOSPHATE ION / Lmo2642 protein
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsJeong, J.H. / Kim, Y.G.
CitationJournal: Proteins / Year: 2011
Title: Structural and Functional Analysis of the Lmo2642 Cyclic Nucleotide Phosphodiesterase from Listeria Monocytogenes.
Authors: Kim, Y.G. / Jeong, J.H. / Ha, N.C. / Kim, K.J.
History
DepositionJul 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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: LMO2642 PROTEIN
B: LMO2642 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,05510
Polymers98,5642
Non-polymers4928
Water9,548530
1
A: LMO2642 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5285
Polymers49,2821
Non-polymers2464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LMO2642 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5285
Polymers49,2821
Non-polymers2464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.963, 103.267, 73.765
Angle α, β, γ (deg.)90.00, 102.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein LMO2642 PROTEIN


Mass: 49281.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q8Y432

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Non-polymers , 5 types, 538 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 7.2 / Details: 20% PEG3350, 0.4M SODIUM FORMATE, pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97957
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 93909 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.5 / % possible all: 63.2

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.7→30 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 4713 4.7 %RANDOM
Rwork0.2118 ---
obs0.2118 93909 93.1 %-
Solvent computationBsol: 35.6467 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.919 Å20 Å2-5.451 Å2
2---3.441 Å20 Å2
3----0.478 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6396 0 16 530 6942
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005173
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_deg1.24721
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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

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