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- PDB-2hpw: Green fluorescent protein from Clytia gregaria -

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Basic information

Entry
Database: PDB / ID: 2hpw
TitleGreen fluorescent protein from Clytia gregaria
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / Fluorescent protein / GFP / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
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 10
Similarity search - Component
Biological speciesClytia gregaria (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsStepanyuk, G. / Liu, Z.J. / Vysotski, S.E. / Lee, J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Crystal Structure of Green Fluorescent Protein from Clytia Gregaria at 1.55 A resolution
Authors: Liu, Z.J. / Markova, S.V. / Frank, L.A. / Stepanyuk, G. / Vysotski, E.S. / Rose, J.P. / Wang, B.C.
History
DepositionJul 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 21, 2015Group: Structure summary
Revision 1.4Aug 30, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / 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.ptnr1_label_atom_id
Revision 2.1Dec 27, 2023Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Remark 999SEQUENCE Currently there is no aminoacid sequence database reference available for the protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,3811
Polymers26,3811
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Green fluorescent protein

A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)52,7612
Polymers52,7612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2540 Å2
ΔGint-12 kcal/mol
Surface area18630 Å2
MethodPISA
3
A: Green fluorescent protein

A: Green fluorescent protein

A: Green fluorescent protein

A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)105,5234
Polymers105,5234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
MethodPQS
Unit cell
Length a, b, c (Å)53.091, 91.446, 110.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-251-

HOH

21A-286-

HOH

31A-352-

HOH

41A-423-

HOH

51A-428-

HOH

61A-435-

HOH

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Components

#1: Protein Green fluorescent protein


Mass: 26380.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clytia gregaria (invertebrata) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: D7PM05*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2 microlitre drops containing protein containing equal volumes of protein solution (9 mg/ml) and precipitate solution (2.0M Ammonium sulfate, 0.1M Citrate), pH 5.5, VAPOR DIFFUSION, SITTING ...Details: 2 microlitre drops containing protein containing equal volumes of protein solution (9 mg/ml) and precipitate solution (2.0M Ammonium sulfate, 0.1M Citrate), pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 2005 / Details: Rosenbaum
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.47→27.7 Å / Num. obs: 40289 / % possible obs: 86.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rsym value: 0.049 / Net I/σ(I): 14.7
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 1.5 % / Num. unique all: 927 / Rsym value: 0.145 / % possible all: 20.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QV1

1qv1


Resolution: 1.55→10 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.376 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20254 1877 4.9 %RANDOM
Rwork0.18169 ---
all0.18271 36117 --
obs0.18271 36117 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.265 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 0 235 2062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221875
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9612541
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58324.30286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8315305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.813157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021440
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.2831
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21251
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2175
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8221160
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.48531822
X-RAY DIFFRACTIONr_scbond_it2.1082833
X-RAY DIFFRACTIONr_scangle_it3.0563719
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 88 -
Rwork0.442 1870 -
obs--69.9 %

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