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- PDB-5drg: Green/cyan WasCFP at pH 10.0 -

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Basic information

Entry
Database: PDB / ID: 5drg
TitleGreen/cyan WasCFP at pH 10.0
ComponentsGreen/cyan WasCFP_pH10 at pH 10.0
KeywordsFLUORESCENT PROTEIN / Green/cyan fluorescent protein / anionic Trp based chromophore / pH and T dependence
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
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
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea coerulescens (belt jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsPletnev, V.Z. / Pletneva, N.V. / Pletnev, S.V.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian Foundation for Basic Research14-04-00004 Russian Federation
Molecular Cell Biology Fund Russian Federation
CitationJournal: Russ.J.Bioorganic Chem. / Year: 2016
Title: Crystal structure of pH and T dependent green fluorescent protein WasCFP with Trp based chromophore
Authors: Pletnev, V.Z. / Pletneva, N. / Efremov, R.G. / Goryacheva, E.A. / Artemyev, I.V. / Arkhipova, S.F. / Sarkisyan, K.S. / Mishin, A.S. / Lukyanov, K.A. / Pletnev, S.V.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact ...pdbx_audit_support / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_conn
Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green/cyan WasCFP_pH10 at pH 10.0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1753
Polymers28,0601
Non-polymers1152
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-17 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.994, 51.289, 47.940
Angle α, β, γ (deg.)90.000, 95.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Green/cyan WasCFP_pH10 at pH 10.0


Mass: 28059.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea coerulescens (belt jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: P42212*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Citric acid pH 5.5, 1 M LiCl, 30 % PEG 6000. Prior to data collection the pH of cryoprotectant was adjusted to 10.0 by 4 M Tris base.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.14→30 Å / Num. obs: 77134 / % possible obs: 97.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Χ2: 0.953 / Net I/av σ(I): 20.22 / Net I/σ(I): 9.4 / Num. measured all: 283181
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.14-1.183.20.34368380.91387.2
1.18-1.233.60.29776760.88197.1
1.23-1.283.70.23976550.88697.5
1.28-1.353.70.19577150.87598.1
1.35-1.443.70.15577850.8998.6
1.44-1.553.70.10878300.91399
1.55-1.73.70.07978320.99499.4
1.7-1.953.80.07679021.0599.7
1.95-2.463.80.05879321.056100
2.46-303.70.03479691.04798.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DQM

5dqm


Resolution: 1.14→21.64 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1616 / WRfactor Rwork: 0.1341 / FOM work R set: 0.9164 / SU B: 0.994 / SU ML: 0.021 / SU R Cruickshank DPI: 0.0316 / SU Rfree: 0.0331 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1646 2316 3 %RANDOM
Rwork0.1346 ---
obs0.1355 74700 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.26 Å2 / Biso mean: 12.626 Å2 / Biso min: 4.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å2-0.24 Å2
2---0.58 Å2-0 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 1.14→21.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 7 298 2117
Biso mean--34.49 27.12 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191987
X-RAY DIFFRACTIONr_bond_other_d0.0020.021883
X-RAY DIFFRACTIONr_angle_refined_deg2.3171.9762705
X-RAY DIFFRACTIONr_angle_other_deg1.06334368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9255253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47525.43592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74715355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.559157
X-RAY DIFFRACTIONr_chiral_restr0.1460.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212319
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02450
X-RAY DIFFRACTIONr_rigid_bond_restr15.11533870
X-RAY DIFFRACTIONr_sphericity_free26.306560
X-RAY DIFFRACTIONr_sphericity_bonded8.94754055
LS refinement shellResolution: 1.143→1.172 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 152 -
Rwork0.213 5135 -
all-5287 -
obs--91.66 %

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