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- PDB-4w6u: Crystal Structure of Full-Length Split GFP Mutant E115H/T118H Wit... -

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Basic information

Entry
Database: PDB / ID: 4w6u
TitleCrystal Structure of Full-Length Split GFP Mutant E115H/T118H With Nickel Mediated Crystal Contacts, P 21 21 21 Space Group
Componentsfluorescent protein E115H/T118H
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / CITRIC ACID / NICKEL (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsLeibly, D.J. / Waldo, G.S. / Yeates, T.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098177 United States
CitationJournal: Structure / Year: 2015
Title: A Suite of Engineered GFP Molecules for Oligomeric Scaffolding.
Authors: Leibly, D.J. / Arbing, M.A. / Pashkov, I. / DeVore, N. / Waldo, G.S. / Terwilliger, T.C. / Yeates, T.O.
History
DepositionAug 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_conn_type.id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 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: fluorescent protein E115H/T118H
B: fluorescent protein E115H/T118H
C: fluorescent protein E115H/T118H
D: fluorescent protein E115H/T118H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8439
Polymers104,4104
Non-polymers4345
Water2,216123
1
A: fluorescent protein E115H/T118H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2854
Polymers26,1021
Non-polymers1833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: fluorescent protein E115H/T118H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1612
Polymers26,1021
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: fluorescent protein E115H/T118H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2952
Polymers26,1021
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: fluorescent protein E115H/T118H


Theoretical massNumber of molelcules
Total (without water)26,1021
Polymers26,1021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.640, 116.580, 165.980
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
fluorescent protein E115H/T118H


Mass: 26102.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.2M NaCl, 0.1M Phosphate-citrate pH 4.2, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.278→82.99 Å / Num. obs: 42930 / % possible obs: 99.3 % / Redundancy: 6.5 % / Rsym value: 0.1054 / Net I/σ(I): 14.2

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: DEV_1555) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 2.28→82.99 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 4292 10 %
Rwork0.21 --
obs0.214 42926 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→82.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7171 0 23 123 7317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017365
X-RAY DIFFRACTIONf_angle_d1.4339951
X-RAY DIFFRACTIONf_dihedral_angle_d16.4252728
X-RAY DIFFRACTIONf_chiral_restr0.0811065
X-RAY DIFFRACTIONf_plane_restr0.0071288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.278-2.30410.35481140.31471043X-RAY DIFFRACTION83
2.3041-2.33120.30361420.27271273X-RAY DIFFRACTION100
2.3312-2.35970.30871440.2451294X-RAY DIFFRACTION100
2.3597-2.38950.2781420.23811282X-RAY DIFFRACTION100
2.3895-2.4210.31871390.24041252X-RAY DIFFRACTION100
2.421-2.45410.24661410.24451271X-RAY DIFFRACTION100
2.4541-2.48920.27591430.2441285X-RAY DIFFRACTION100
2.4892-2.52640.31571430.24091285X-RAY DIFFRACTION100
2.5264-2.56580.31771400.23831264X-RAY DIFFRACTION100
2.5658-2.60790.31051430.24491279X-RAY DIFFRACTION100
2.6079-2.65290.27641440.24631304X-RAY DIFFRACTION100
2.6529-2.70110.29411410.23141262X-RAY DIFFRACTION100
2.7011-2.75310.30011410.22611271X-RAY DIFFRACTION100
2.7531-2.80930.27381450.24311304X-RAY DIFFRACTION100
2.8093-2.87040.31891410.23431268X-RAY DIFFRACTION100
2.8704-2.93710.27861430.23751290X-RAY DIFFRACTION100
2.9371-3.01060.29311430.23421285X-RAY DIFFRACTION100
3.0106-3.0920.2991410.22171273X-RAY DIFFRACTION99
3.092-3.1830.26741450.22111303X-RAY DIFFRACTION100
3.183-3.28570.27141400.20781260X-RAY DIFFRACTION100
3.2857-3.40320.22831490.21071343X-RAY DIFFRACTION100
3.4032-3.53940.24911420.21011276X-RAY DIFFRACTION100
3.5394-3.70050.24271450.19391300X-RAY DIFFRACTION100
3.7005-3.89560.24821430.20031293X-RAY DIFFRACTION100
3.8956-4.13970.24591460.19311310X-RAY DIFFRACTION100
4.1397-4.45930.18141450.17791310X-RAY DIFFRACTION100
4.4593-4.9080.20081480.16051329X-RAY DIFFRACTION100
4.908-5.61810.1881490.18621337X-RAY DIFFRACTION100
5.6181-7.07760.24591500.21271356X-RAY DIFFRACTION100
7.0776-83.04510.26251600.22271432X-RAY DIFFRACTION99
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)
13.89330.54860.45822.6144-0.22012.10660.0094-0.01740.01810.0156-0.02070.0131-0.0563-0.01110.01910.3166-0.0167-0.03620.2747-0.01530.224-0.3646-9.634642.2877
23.433-0.519-0.08252.37250.14092.3906-0.09820.02330.0709-0.01190.0245-0.1253-0.00220.0190.07060.30390.0030.00790.2611-0.02040.28023.726616.309320.5156
34.1415-0.2387-0.98571.98890.14022.2898-0.22830.4181-0.54020.04660.05230.04630.2514-0.27670.11050.3783-0.06430.08540.3752-0.10430.354910.34321.7444-4.6481
44.11460.78480.32732.37160.62482.245-0.07710.7346-0.4969-0.20350.145-0.22920.144-0.118-0.02860.4215-0.06060.02280.4311-0.11160.3875-7.6845-33.37925.0522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 4:229)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 4:227)
3X-RAY DIFFRACTION3(CHAIN C AND RESSEQ 4:228)
4X-RAY DIFFRACTION4(CHAIN D AND RESSEQ 3:228)

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