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- PDB-5dqm: Green/cyan WasCFP at pH 2.0 -

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Basic information

Entry
Database: PDB / ID: 5dqm
TitleGreen/cyan WasCFP at pH 2.0
ComponentsWasCFP_pH2
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: 1.3 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 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WasCFP_pH2


Theoretical massNumber of molelcules
Total (without water)28,0601
Polymers28,0601
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-3 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.268, 51.528, 47.529
Angle α, β, γ (deg.)90.000, 97.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein WasCFP_pH2


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2
Details: 0.1 M Citric acid pH 5.5, 1 M LiCl, 30 % PEG 6000. Prior to data collection pH of the cryoprotectant was adjusted to 2.0 by citric acid

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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: 1.3→30 Å / Num. obs: 53938 / % possible obs: 96.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.048 / Χ2: 0.893 / Net I/av σ(I): 25.542 / Net I/σ(I): 9.6 / Num. measured all: 205757
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.3-1.353.60.58252070.80493.6
1.35-1.43.80.50552960.83794.7
1.4-1.463.90.35552750.84995.2
1.46-1.543.90.23753110.81295.8
1.54-1.643.90.15754080.82796.2
1.64-1.763.90.11553890.88696.8
1.76-1.943.80.0854260.99197.4
1.94-2.223.80.05854960.9898
2.22-2.83.80.04155760.95698.7
2.8-303.70.02255540.9797.4

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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: 5DQB

5dqb


Resolution: 1.3→22.28 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1929 / WRfactor Rwork: 0.1632 / FOM work R set: 0.796 / SU B: 2.626 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0525 / SU Rfree: 0.0544 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 1093 2 %RANDOM
Rwork0.1622 ---
obs0.1632 52764 96.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.94 Å2 / Biso mean: 17.335 Å2 / Biso min: 7.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å2-0.04 Å2
2--0.07 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.3→22.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 0 167 1979
Biso mean---25.92 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0191933
X-RAY DIFFRACTIONr_bond_other_d0.0020.021824
X-RAY DIFFRACTIONr_angle_refined_deg2.5051.9742626
X-RAY DIFFRACTIONr_angle_other_deg1.19134227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8075242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3425.60491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06315341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.161156
X-RAY DIFFRACTIONr_chiral_restr0.1810.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212234
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02434
X-RAY DIFFRACTIONr_rigid_bond_restr11.65733757
X-RAY DIFFRACTIONr_sphericity_free16.983574
X-RAY DIFFRACTIONr_sphericity_bonded14.46953802
LS refinement shellResolution: 1.298→1.331 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 59 -
Rwork0.217 3685 -
all-3744 -
obs--91.61 %

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