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- PDB-5hzu: Crystal structure of Dronpa-Ni2+ -

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Basic information

Entry
Database: PDB / ID: 5hzu
TitleCrystal structure of Dronpa-Ni2+
ComponentsFluorescent protein DronpaFluorescence
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
NICKEL (II) ION / Fluorescent protein Dronpa
Similarity search - Component
Biological speciesEchinophyllia sp. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 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 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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)297,32537
Polymers295,85712
Non-polymers1,46725
Water36,1022004
1
A: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7723
Polymers24,6551
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area9670 Å2
MethodPISA
2
B: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7723
Polymers24,6551
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area9960 Å2
MethodPISA
3
C: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7723
Polymers24,6551
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area9660 Å2
MethodPISA
4
D: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7723
Polymers24,6551
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area9630 Å2
MethodPISA
5
E: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7723
Polymers24,6551
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area9830 Å2
MethodPISA
6
F: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7723
Polymers24,6551
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area9650 Å2
MethodPISA
7
G: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7723
Polymers24,6551
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area9640 Å2
MethodPISA
8
H: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7723
Polymers24,6551
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area9800 Å2
MethodPISA
9
I: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7723
Polymers24,6551
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area9640 Å2
MethodPISA
10
J: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7723
Polymers24,6551
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area9680 Å2
MethodPISA
11
K: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8314
Polymers24,6551
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area9630 Å2
MethodPISA
12
L: Fluorescent protein Dronpa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7723
Polymers24,6551
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.372, 109.403, 72.087
Angle α, β, γ (deg.)71.110, 85.970, 61.300
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Fluorescent protein Dronpa / Fluorescence


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-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2004 / 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: 46.95 %
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: 1.89→30 Å / Num. obs: 198444 / % possible obs: 94.9 % / Redundancy: 3 % / Net I/σ(I): 22.185

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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: 1.89→29.03 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.208 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.136
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 9967 5 %RANDOM
Rwork0.1509 ---
obs0.1534 188475 93.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.15 Å2 / Biso mean: 24.27 Å2 / Biso min: 10.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20.11 Å2-0.04 Å2
2---0.49 Å2-0.19 Å2
3---1.15 Å2
Refinement stepCycle: final / Resolution: 1.89→29.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20706 0 25 2004 22735
Biso mean--36.31 31.23 -
Num. residues----2563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01921282
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219632
X-RAY DIFFRACTIONr_angle_refined_deg2.0641.96128692
X-RAY DIFFRACTIONr_angle_other_deg0.893345390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16752527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05124.5041048
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.707153575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5261584
X-RAY DIFFRACTIONr_chiral_restr0.1240.22911
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02124029
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024999
X-RAY DIFFRACTIONr_mcbond_it2.0382.1310216
X-RAY DIFFRACTIONr_mcbond_other2.0352.1310215
X-RAY DIFFRACTIONr_mcangle_it2.7993.18612683
LS refinement shellResolution: 1.895→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 588 -
Rwork0.221 11752 -
all-12340 -
obs--78.86 %

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