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- PDB-5gl4: Crystal structure of TON_0340 in complex with Mn -

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Basic information

Entry
Database: PDB / ID: 5gl4
TitleCrystal structure of TON_0340 in complex with Mn
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / TON_0340 / Thermococcus onnurineus / Mn2+-dependent phosphatase
Function / homology
Function and homology information


D-glutamate cyclase activity / glutamate metabolic process / metal ion binding
Similarity search - Function
TON_0340 / D-glutamate cyclase-like, C-terminal / D-glutamate cyclase-like, C-terminal / inorganic pyrophosphatase (n-terminal core) / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / D-glutamate cyclase-like C-terminal domain-containing protein
Similarity search - Component
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 8, 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 / diffrn_source
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site
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 / _struct_conn.ptnr2_label_seq_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)175,57923
Polymers174,6456
Non-polymers93417
Water4,720262
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4907
Polymers58,2152
Non-polymers2755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-44 kcal/mol
Surface area19470 Å2
MethodPISA
2
C: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5458
Polymers58,2152
Non-polymers3306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-51 kcal/mol
Surface area19450 Å2
MethodPISA
3
D: Uncharacterized protein
E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5458
Polymers58,2152
Non-polymers3306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-35 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.041, 107.041, 360.961
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 (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0340 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YTD8
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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, manganese chloride

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 112616 / % possible obs: 82.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.063 / Χ2: 2.004 / Net I/av σ(I): 19.88 / Net I/σ(I): 15 / Num. measured all: 443354
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.03-2.071.50.31535171.71652.3
2.07-2.11.60.28440501.13759.9
2.1-2.141.70.26440750.97860.8
2.14-2.191.80.27443331.09164.1
2.19-2.231.90.25945281.11767.1
2.23-2.292.10.25847861.24471
2.29-2.342.20.23650731.17975.2
2.34-2.412.40.22752341.21177.3
2.41-2.482.60.20454161.2579.9
2.48-2.562.90.19156901.30684.2
2.56-2.653.30.1758831.32986.5
2.65-2.763.50.15160971.36389.2
2.76-2.883.90.12861991.41791.4
2.88-3.034.30.10764451.51194.1
3.03-3.224.80.08765561.58695.9
3.22-3.475.60.07467441.86997.9
3.47-3.826.20.07268062.75598.5
3.82-4.376.30.06568623.25198.8
4.37-5.516.70.05570022.78299.2
5.51-506.80.03573201.81898.3

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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: 2.2→50 Å / Cross valid method: FREE R-VALUE / σ(F): 38
RfactorNum. reflection% reflection
Rfree0.259 4804 4.5 %
Rwork0.217 90194 -
obs-94998 88.4 %
Solvent computationBsol: 27.5887 Å2
Displacement parametersBiso max: 121.85 Å2 / Biso mean: 41.3897 Å2 / Biso min: 15.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.881 Å20 Å20 Å2
2---0.881 Å20 Å2
3---1.762 Å2
Refinement stepCycle: final / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12087 0 17 262 12366
Biso mean--55.75 37.31 -
Num. residues----1590
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3121.5
X-RAY DIFFRACTIONc_scbond_it2.0512
X-RAY DIFFRACTIONc_mcangle_it2.1782
X-RAY DIFFRACTIONc_scangle_it3.1262.5
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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