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- PDB-5gl3: Crystal structure of TON_0340 in complex with Mg -

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Basic information

Entry
Database: PDB / ID: 5gl3
TitleCrystal structure of TON_0340 in complex with Mg
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / TON_0340 / Thermococcus onnurineus / Mn2+-dependent phosphatase
Function / homologyTON_0340 / D-glutamate cyclase-like, C-terminal / D-glutamate cyclase-like, C-terminal / inorganic pyrophosphatase (n-terminal core) / Alpha-Beta Complex / metal ion binding / Alpha Beta / D-glutamate cyclase-like C-terminal domain-containing protein
Function and homology information
Biological speciesThermococcus onnurineus NA1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLee, S.G. / Sohn, Y.S. / Oh, B.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Oceans and Fisheries Korea, Republic Of
Citation
Journal: PLoS ONE / Year: 2016
Title: Identification of a Highly Conserved Hypothetical Protein TON_0340 as a Probable Manganese-Dependent Phosphatase.
Authors: Sohn, Y.S. / Lee, S.G. / Lee, K.H. / Ku, B. / Shin, H.C. / Cha, S.S. / Kim, Y.G. / Lee, H.S. / Kang, S.G. / Oh, B.H.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Experimental phasing using zinc anomalous scattering.
Authors: Cha, S.S. / An, Y.J. / Jeong, C.S. / Kim, M.K. / Lee, S.G. / Lee, K.H. / Oh, B.H.
History
DepositionJul 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,93718
Polymers174,6456
Non-polymers29212
Water3,783210
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3126
Polymers58,2152
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3126
Polymers58,2152
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Uncharacterized protein
E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3126
Polymers58,2152
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.982, 106.982, 363.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Uncharacterized protein


Mass: 29107.531 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus NA1 (archaea) / Strain: NA1 / Gene: TON_0340 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YTD8
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: sodium acetate pH, 16% 2-methyl-2,4-pentanediol,magnesium acetate

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 73586 / % possible obs: 87.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.061 / Χ2: 2.114 / Net I/av σ(I): 31.136 / Net I/σ(I): 16.2 / Num. measured all: 423552
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.442.50.20326610.91264.4
2.44-2.492.70.19928010.96668.1
2.49-2.532.90.18828811.02770.8
2.53-2.5930.17230731.02674.7
2.59-2.643.20.16631981.09377.4
2.64-2.73.50.15932691.13379.2
2.7-2.773.80.14734681.23784.2
2.77-2.854.10.13735461.34885.6
2.85-2.934.50.12636101.44787.4
2.93-3.0250.11537691.58690.5
3.02-3.135.40.10838621.79392.8
3.13-3.265.90.139231.9894.4
3.26-3.416.50.0940052.27196
3.41-3.587.20.0840842.50797.3
3.58-3.817.60.07340942.58497.6
3.81-4.180.06641502.5798.2
4.1-4.528.50.0641712.7198.7
4.52-5.178.50.05542072.54698.6
5.17-6.517.90.04842731.92898.2
6.51-508.60.03345412.49498

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FC5

4fc5


Resolution: 2.4→50 Å / Cross valid method: FREE R-VALUE / σ(F): 30
RfactorNum. reflection% reflection
Rfree0.243 3738 4.5 %
Rwork0.199 69784 -
obs-73552 87.8 %
Solvent computationBsol: 28.9921 Å2
Displacement parametersBiso max: 100.91 Å2 / Biso mean: 43.3875 Å2 / Biso min: 15.67 Å2
Baniso -1Baniso -2Baniso -3
1--2.308 Å20 Å20 Å2
2---2.308 Å20 Å2
3---4.617 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12196 0 12 210 12418
Biso mean--47.32 37.11 -
Num. residues----1604
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2631.5
X-RAY DIFFRACTIONc_scbond_it2.0212
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scangle_it3.0282.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param

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