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- PDB-5hzs: Crystal structure of Dronpa-Co2+ -

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Basic information

Entry
Database: PDB / ID: 5hzs
TitleCrystal structure of Dronpa-Co2+
ComponentsFluorescent protein Dronpa
KeywordsLUMINESCENT PROTEIN / Fluorescent Protein
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / identical protein binding / metal ion binding
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Fluorescent protein Dronpa
Similarity search - Component
Biological speciesEchinophyllia sp. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.17 Å
AuthorsHwang, K.Y. / Nam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)NRF-2014R1A1A2059440 Korea, Republic Of
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)NRF-2014R1212513 Korea, Republic Of
CitationJournal: FEBS Lett. / Year: 2016
Title: Crystal structures of Dronpa complexed with quenchable metal ions provide insight into metal biosensor development
Authors: Kim, I.J. / Kim, S. / Park, J. / Eom, I. / Kim, S. / Kim, J.H. / Ha, S.C. / Kim, Y.G. / Hwang, K.Y. / Nam, K.H.
History
DepositionFeb 3, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Nov 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_symmetry
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorescent protein Dronpa
B: Fluorescent protein Dronpa
C: Fluorescent protein Dronpa
D: Fluorescent protein Dronpa
E: Fluorescent protein Dronpa
F: Fluorescent protein Dronpa
G: Fluorescent protein Dronpa
H: Fluorescent protein Dronpa
I: Fluorescent protein Dronpa
J: Fluorescent protein Dronpa
K: Fluorescent protein Dronpa
L: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,27236
Polymers295,85712
Non-polymers1,41424
Water24,2481346
1
A: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7733
Polymers24,6551
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area9820 Å2
MethodPISA
2
B: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7733
Polymers24,6551
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area9760 Å2
MethodPISA
3
C: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7733
Polymers24,6551
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area9920 Å2
MethodPISA
4
D: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7733
Polymers24,6551
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area9830 Å2
MethodPISA
5
E: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7733
Polymers24,6551
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area9800 Å2
MethodPISA
6
F: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7733
Polymers24,6551
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area9860 Å2
MethodPISA
7
G: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7733
Polymers24,6551
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area9760 Å2
MethodPISA
8
H: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7733
Polymers24,6551
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area9680 Å2
MethodPISA
9
I: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7733
Polymers24,6551
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area9690 Å2
MethodPISA
10
J: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7733
Polymers24,6551
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area9780 Å2
MethodPISA
11
K: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7733
Polymers24,6551
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area9660 Å2
MethodPISA
12
L: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7733
Polymers24,6551
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.330, 105.479, 109.776
Angle α, β, γ (deg.)115.790, 109.510, 93.950
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Fluorescent protein Dronpa


Mass: 24654.785 Da / Num. of mol.: 12 / Fragment: UNP residues 2-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5TLG6
#2: Chemical...
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1346 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4000, Tris-HCl, MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→30 Å / Num. obs: 130970 / % possible obs: 95.1 % / Redundancy: 3.1 % / Net I/σ(I): 25.02

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GX2

2gx2


Resolution: 2.17→29.57 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.235 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.215
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 6546 5 %RANDOM
Rwork0.1659 ---
obs0.1689 124396 93.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.3 Å2 / Biso mean: 31.303 Å2 / Biso min: 11.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å2-0.37 Å2-2.1 Å2
2--0.07 Å2-0.6 Å2
3----0.36 Å2
Refinement stepCycle: final / Resolution: 2.17→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20748 0 24 1346 22118
Biso mean--48.21 33.46 -
Num. residues----2569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01921324
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219660
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.96128748
X-RAY DIFFRACTIONr_angle_other_deg0.857345460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.66552533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43424.5141050
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2153583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6571584
X-RAY DIFFRACTIONr_chiral_restr0.1080.22917
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02124079
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025005
X-RAY DIFFRACTIONr_mcbond_it2.4152.91310240
X-RAY DIFFRACTIONr_mcbond_other2.4142.91310239
X-RAY DIFFRACTIONr_mcangle_it3.4874.36112713
LS refinement shellResolution: 2.172→2.229 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 337 -
Rwork0.241 6682 -
all-7019 -
obs--67.38 %

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