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- PDB-5mse: GFP nuclear transport receptor mimic 3B8 -

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Basic information

Entry
Database: PDB / ID: 5mse
TitleGFP nuclear transport receptor mimic 3B8
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP Nuclear transport receptor
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
IMIDAZOLE / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsHuyton, T. / Gorlich, D.
CitationJournal: Cell / Year: 2018
Title: Surface Properties Determining Passage Rates of Proteins through Nuclear Pores.
Authors: Frey, S. / Rees, R. / Schunemann, J. / Ng, S.C. / Funfgeld, K. / Huyton, T. / Gorlich, D.
History
DepositionJan 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct / Item: _citation.title / _struct.title
Revision 1.2May 15, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 1.3Jan 17, 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 / struct_ncs_dom_lim
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_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.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_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
C: Green fluorescent protein
D: Green fluorescent protein
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,85716
Polymers110,3964
Non-polymers46012
Water14,196788
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-133 kcal/mol
Surface area35350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.401, 73.398, 93.927
Angle α, β, γ (deg.)90.00, 93.73, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22D
13A
23B
14A
24C
15A
25D
16A
26B
17C
27D
18C
28B
19C
29D
110C
210B
111D
211B
112D
212B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYTHRTHRAA4 - 636 - 65
21GLYGLYTHRTHRCB4 - 636 - 65
12GLYGLYLEULEUAA4 - 646 - 66
22GLYGLYLEULEUDC4 - 646 - 66
13GLYGLYLEULEUAA4 - 646 - 66
23GLYGLYLEULEUBD4 - 646 - 66
14VALVALGLYGLYAA68 - 22868 - 228
24VALVALGLYGLYCB68 - 22868 - 228
15VALVALILEILEAA68 - 22968 - 229
25VALVALILEILEDC68 - 22968 - 229
16VALVALILEILEAA68 - 22968 - 229
26VALVALILEILEBD68 - 22968 - 229
17GLYGLYTHRTHRCB4 - 636 - 65
27GLYGLYTHRTHRDC4 - 636 - 65
18GLYGLYTHRTHRCB4 - 636 - 65
28GLYGLYTHRTHRBD4 - 636 - 65
19VALVALGLYGLYCB68 - 22868 - 228
29VALVALGLYGLYDC68 - 22868 - 228
110VALVALGLYGLYCB68 - 22868 - 228
210VALVALGLYGLYBD68 - 22868 - 228
111GLYGLYLEULEUDC4 - 646 - 66
211GLYGLYLEULEUBD4 - 646 - 66
112VALVALILEILEDC68 - 22968 - 229
212VALVALILEILEBD68 - 22968 - 229

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Green fluorescent protein


Mass: 27599.092 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P42212
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 788 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 5-9% PEG8000, 28% glycerol, 100?mM Imidazole (pH 7.1)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2016 / Details: 50 x 50?M
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.664→46.28 Å / Num. obs: 114871 / % possible obs: 98.38 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1287 / Net I/σ(I): 12.47
Reflection shellResolution: 1.664→1.723 Å / Redundancy: 7 % / Rmerge(I) obs: 1.91 / Mean I/σ(I) obs: 1.18 / CC1/2: 0.468 / % possible all: 96.49

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMA

1ema


Resolution: 1.66→46.86 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.7 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20573 5744 5 %RANDOM
Rwork0.17375 ---
obs0.17532 109127 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.711 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.67 Å2
2---0.54 Å20 Å2
3---1 Å2
Refinement stepCycle: 1 / Resolution: 1.66→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7327 0 28 788 8143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0197560
X-RAY DIFFRACTIONr_bond_other_d0.0020.026742
X-RAY DIFFRACTIONr_angle_refined_deg2.3181.95510227
X-RAY DIFFRACTIONr_angle_other_deg1.1922.99815511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2645895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.42422.596416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.425151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1861588
X-RAY DIFFRACTIONr_chiral_restr0.1630.21071
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0218522
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021754
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8241.913580
X-RAY DIFFRACTIONr_mcbond_other1.8211.9093579
X-RAY DIFFRACTIONr_mcangle_it2.6312.8534463
X-RAY DIFFRACTIONr_mcangle_other2.6312.8544464
X-RAY DIFFRACTIONr_scbond_it3.6462.4213980
X-RAY DIFFRACTIONr_scbond_other3.6462.4213981
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7253.455761
X-RAY DIFFRACTIONr_long_range_B_refined8.49824.7878461
X-RAY DIFFRACTIONr_long_range_B_other8.49924.7598457
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A31680.07
12C31680.07
21A32720.06
22D32720.06
31A32920.05
32B32920.05
41A103840.06
42C103840.06
51A105260.05
52D105260.05
61A105200.05
62B105200.05
71C31560.05
72D31560.05
81C31880.05
82B31880.05
91C104420.05
92D104420.05
101C104220.06
102B104220.06
111D32760.05
112B32760.05
121D104440.06
122B104440.06
LS refinement shellResolution: 1.664→1.707 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 414 -
Rwork0.413 7865 -
obs--95.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.50380.0554-0.05220.26180.09470.3779-0.0081-0.0645-0.15510.035-0.0092-0.0734-0.0523-0.00960.01730.01930.0018-0.01250.01710.0290.0734-47.123514.844221.519
20.18560.04360.09720.52930.05260.44720.0138-0.0201-0.02770.0709-0.01880.08450.00870.02680.0050.0146-0.00320.01850.02850.00430.037-76.007927.80921.6532
30.26630.0107-0.09860.506-0.08850.41860.0037-0.03370.04360.0731-0.0337-0.1525-0.0076-0.03740.030.0177-0.0052-0.0310.0193-0.00080.0688-34.108443.728621.4931
40.4413-0.02260.05110.282-0.10120.3579-0.0167-0.04130.1060.05070.00240.01120.025-0.01520.01430.02470.00040.00070.0163-0.02310.0405-62.999556.78621.4751
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 229
2X-RAY DIFFRACTION2C2 - 230
3X-RAY DIFFRACTION3D4 - 229
4X-RAY DIFFRACTION4B4 - 229

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