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- PDB-4lw5: Crystal structure of all-trans green fluorescent protein -

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Basic information

Entry
Database: PDB / ID: 4lw5
TitleCrystal structure of all-trans green fluorescent protein
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / 11-stranded beta barrel
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 victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsRosenman, D.J. / Huang, Y.-M. / Xia, K. / Vanroey, P. / Colon, W. / Bystroff, C.
CitationJournal: Protein Sci. / Year: 2014
Title: Green-lighting green fluorescent protein: Faster and more efficient folding by eliminating a cis-trans peptide isomerization event.
Authors: Rosenman, D.J. / Huang, Y.M. / Xia, K. / Fraser, K. / Jones, V.E. / Lamberson, C.M. / Van Roey, P. / Colon, W. / Bystroff, C.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
C: Green fluorescent protein
D: Green fluorescent protein
E: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)134,7025
Polymers134,7025
Non-polymers00
Water7,710428
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9401
Polymers26,9401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9401
Polymers26,9401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9401
Polymers26,9401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9401
Polymers26,9401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9401
Polymers26,9401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.557, 110.939, 114.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Green fluorescent protein


Mass: 26940.346 Da / Num. of mol.: 5 / Fragment: SEE REMARK 999 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FLUOROPHORE (CRO) IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE ...THE FLUOROPHORE (CRO) IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE BETWEEN THE NITROGEN OF GLY 67 AND THE CARBONYL CARBON OF THR 65. THE CARBONYL OXYGEN OF THR 65 LEAVES AS WATER, AND IS NOT PRESENT IN THE MODEL. A SUBSEQUENT OXIDATION OF THE CA - CB BOND OF TYR 66 LINKS THE CONJUGATED SYSTEM OF THE TYROSINE RING TO THAT OF THE FORMED BACKBONE IMIDAZOLIDINONE. RESIDUES 65, 66, AND 67 ARE NOT PRESENT IN THE ENTRY AND ARE INSTEAD REPLACED WITH CRO 66.

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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: 45.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M sodium chloride, 0.1 M HEPES, pH 7.5, 20% w/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 12, 2011
RadiationMonochromator: Bent single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.55→33.826 Å / Num. all: 40443 / Num. obs: 40237 / % possible obs: 99.49 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 27.5 Å2 / Rsym value: 0.119 / Net I/σ(I): 20.2
Reflection shellResolution: 2.55→2.71 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.13 / Rsym value: 0.536 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B3P

2b3p


Resolution: 2.55→19.94 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2811 1999 4.9 %RANDOM
Rwork0.2178 38238 --
obs-40237 99.5 %-
Solvent computationBsol: 25.1599 Å2
Displacement parametersBiso max: 85.48 Å2 / Biso mean: 35.25 Å2 / Biso min: 7.77 Å2
Baniso -1Baniso -2Baniso -3
1-9.586 Å20 Å20 Å2
2---3.79 Å20 Å2
3----5.795 Å2
Refinement stepCycle: LAST / Resolution: 2.55→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8983 0 0 428 9411
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.396
X-RAY DIFFRACTIONc_mcbond_it1.3151.5
X-RAY DIFFRACTIONc_scbond_it1.9532
X-RAY DIFFRACTIONc_mcangle_it2.2632
X-RAY DIFFRACTIONc_scangle_it3.0332.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.640.3391830.28823731391498.4
2.64-2.750.41012070.293537803987100
2.75-2.870.38851950.296938134008100
2.87-3.020.3932020.29873769397199.9
3.02-3.210.30942050.250837984003100
3.21-3.460.31542030.2338314034100
3.46-3.810.28522020.23163821402399.9
3.81-4.360.22481850.19553858404399.7
4.36-5.490.23852010.16183892409399.9
5.49-500.010.19822160.15693945416197.4
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6CNS_TOPPAR:cro.param

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