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- PDB-4dwz: Crystal Structure of Ton_0340 -

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Basic information

Entry
Database: PDB / ID: 4dwz
TitleCrystal Structure of Ton_0340
ComponentsHypothetical protein TON_0340Hypothesis
KeywordsMETAL BINDING PROTEIN
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 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsLee, S.G. / Lee, K.H. / Cha, S.S. / Oh, B.H.
CitationJournal: 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
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Hypothetical protein TON_0340
B: Hypothetical protein TON_0340
C: Hypothetical protein TON_0340
D: Hypothetical protein TON_0340
E: Hypothetical protein TON_0340
F: Hypothetical protein TON_0340
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,13144
Polymers174,6456
Non-polymers2,48638
Water2,144119
1
A: Hypothetical protein TON_0340
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5658
Polymers29,1081
Non-polymers4587
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein TON_0340
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5658
Polymers29,1081
Non-polymers4587
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical protein TON_0340
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3695
Polymers29,1081
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hypothetical protein TON_0340
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4356
Polymers29,1081
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Hypothetical protein TON_0340
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6319
Polymers29,1081
Non-polymers5238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Hypothetical protein TON_0340
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5658
Polymers29,1081
Non-polymers4587
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Hypothetical protein TON_0340
F: Hypothetical protein TON_0340
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,13116
Polymers58,2152
Non-polymers91614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-15 kcal/mol
Surface area20120 Å2
MethodPISA
8
B: Hypothetical protein TON_0340
D: Hypothetical protein TON_0340
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,00014
Polymers58,2152
Non-polymers78512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-18 kcal/mol
Surface area19700 Å2
MethodPISA
9
C: Hypothetical protein TON_0340
E: Hypothetical protein TON_0340
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,00014
Polymers58,2152
Non-polymers78512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-18 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.442, 107.442, 355.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Hypothetical protein TON_0340 / Hypothesis


Mass: 29107.531 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (archaea) / Strain: NA1 / Plasmid: pET22bCPD10H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3-RIPL) / References: UniProt: B6YTD8
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M sodium acetate pH 5.5, 0.35M zinc acetate, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2822 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 58281 / Num. obs: 57476 / % possible obs: 98.6 % / Redundancy: 18 % / Biso Wilson estimate: 51.9 Å2 / Net I/σ(I): 40.125
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 11 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 4.286 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→48.92 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 5835 10 %random
Rwork0.2229 ---
all-58281 --
obs-57476 98.6 %-
Solvent computationBsol: 31.2642 Å2
Displacement parametersBiso mean: 51.3903 Å2
Baniso -1Baniso -2Baniso -3
1-0.822 Å20 Å20 Å2
2--0.822 Å20 Å2
3----1.645 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12044 0 38 119 12201
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.1861.5
X-RAY DIFFRACTIONc_scbond_it1.8542
X-RAY DIFFRACTIONc_mcangle_it2.0342
X-RAY DIFFRACTIONc_scangle_it2.9132.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.333 885 -
Rwork0.281 --
obs-8226 95.8 %
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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