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- PDB-4fc5: Crystal Structure of Ton_0340 -

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Basic information

Entry
Database: PDB / ID: 4fc5
TitleCrystal Structure of Ton_0340
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION
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: 2.3 Å
AuthorsLee, S.G. / Lee, K.H. / An, Y.J. / 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
DepositionMay 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Mar 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)178,88759
Polymers175,4206
Non-polymers3,46753
Water25,9961443
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7609
Polymers29,2371
Non-polymers5238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,95612
Polymers29,2371
Non-polymers71911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7609
Polymers29,2371
Non-polymers5238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6958
Polymers29,2371
Non-polymers4587
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,95612
Polymers29,2371
Non-polymers71911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7609
Polymers29,2371
Non-polymers5238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Putative uncharacterized protein
F: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,52018
Polymers58,4732
Non-polymers1,04716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-16 kcal/mol
Surface area19660 Å2
MethodPISA
8
B: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,65120
Polymers58,4732
Non-polymers1,17718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-16 kcal/mol
Surface area19290 Å2
MethodPISA
9
C: Putative uncharacterized protein
E: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,71621
Polymers58,4732
Non-polymers1,24319
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-17 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.181, 107.181, 356.384
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
Putative uncharacterized protein / TON_0340


Mass: 29236.713 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (archaea) / Strain: NA1 / Gene: TON_0340 / Plasmid: pET22b / 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.: 53 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1443 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 5% (v/v) isopropanol, 100mM sodium acetate (pH 5.0), 350mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2822 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2010
RadiationMonochromator: Zn wevelength / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 93390 / Num. obs: 87763 / % possible obs: 94 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: -1.8 Å2
Reflection shellResolution: 2.3→2.34 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→44.45 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 44948.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.281 8780 10 %RANDOM
Rwork0.223 ---
obs0.223 87763 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.112 Å2 / ksol: 0.311203 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2---1.44 Å20 Å2
3---2.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12036 0 53 1443 13532
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
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
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.438 1292 9.9 %
Rwork0.418 11781 -
obs--85.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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