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- PDB-5gl2: Crystal structure of TON_0340 in complex with Ca -

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Basic information

Entry
Database: PDB / ID: 5gl2
TitleCrystal structure of TON_0340 in complex with Ca
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: 2.03 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.,Sect.D / 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 / 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 / _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)174,88612
Polymers174,6456
Non-polymers2406
Water5,675315
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2954
Polymers58,2152
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-42 kcal/mol
Surface area19150 Å2
MethodPISA
2
C: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2954
Polymers58,2152
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-39 kcal/mol
Surface area19200 Å2
MethodPISA
3
D: Uncharacterized protein
E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2954
Polymers58,2152
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-32 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.840, 106.840, 364.019
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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, 2-methyl-2,4-pentanediol, calcium choloride

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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: 2.03→50 Å / Num. obs: 124949 / % possible obs: 91.2 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.102 / Net I/av σ(I): 42.881 / Net I/σ(I): 20.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.03-2.072.60.205177.1
2.07-2.12.80.191181.9
2.1-2.1430.182183.7
2.14-2.193.20.165186.6
2.19-2.233.30.152188.2
2.23-2.293.50.143190.3
2.29-2.343.70.137191.3
2.34-2.413.90.13192.6
2.41-2.484.10.125193.2
2.48-2.564.40.117194.2
2.56-2.654.70.111194.9
2.65-2.764.90.107195
2.76-2.885.30.104195.3
2.88-3.035.70.099195.3
3.03-3.226.10.098195.7
3.22-3.476.40.099195.5
3.47-3.826.90.107195.2
3.82-4.377.30.115194.8
4.37-5.517.40.098193.9
5.51-507.40.086189.5

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Processing

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

4fc5


Resolution: 2.03→50 Å / Cross valid method: FREE R-VALUE / σ(F): 30
RfactorNum. reflection% reflection
Rfree0.2495 12466 9.1 %
Rwork0.2192 --
obs0.315 124912 91.3 %
Solvent computationBsol: 51.6567 Å2
Displacement parametersBiso max: 89.43 Å2 / Biso mean: 37.3969 Å2 / Biso min: 15.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.585 Å20 Å20 Å2
2--0.585 Å20 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 2.03→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12198 0 6 315 12519
Biso mean--36.91 35.61 -
Num. residues----1606
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_scbond_it2.0622
X-RAY DIFFRACTIONc_mcangle_it2.0222
X-RAY DIFFRACTIONc_scangle_it2.9522.5
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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