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- PDB-4w7d: Crystal Structure of Full-Length Split GFP Mutant D21H/K26H With ... -

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Basic information

Entry
Database: PDB / ID: 4w7d
TitleCrystal Structure of Full-Length Split GFP Mutant D21H/K26H With Copper Mediated Crystal Contacts, P 21 21 21 Space Group
Componentsfluorescent protein D21H/K26H
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / COPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 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.country ..._citation.journal_id_CSD / _pdbx_audit_support.country / _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 / struct_conn / struct_conn_type
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.pdbx_ptnr1_label_alt_id / _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 23, 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 D21H/K26H
B: fluorescent protein D21H/K26H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,31012
Polymers52,2412
Non-polymers1,07010
Water5,567309
1
A: fluorescent protein D21H/K26H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7037
Polymers26,1201
Non-polymers5826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: fluorescent protein D21H/K26H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6085
Polymers26,1201
Non-polymers4884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.420, 82.050, 113.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein fluorescent protein D21H/K26H


Mass: 26120.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 319 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 20% PEG8000, 0.1M CHES pH9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.799→66.57 Å / Num. obs: 49634 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rsym value: 0.138 / Net I/σ(I): 8.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1555)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.8→66.57 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 4963 10 %
Rwork0.179 --
obs0.183 49628 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→66.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 58 309 3985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073814
X-RAY DIFFRACTIONf_angle_d1.3215157
X-RAY DIFFRACTIONf_dihedral_angle_d14.3631429
X-RAY DIFFRACTIONf_chiral_restr0.048554
X-RAY DIFFRACTIONf_plane_restr0.006659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.799-1.81960.37691500.35041344X-RAY DIFFRACTION89
1.8196-1.8410.30931600.30461446X-RAY DIFFRACTION100
1.841-1.86350.34071640.29571471X-RAY DIFFRACTION100
1.8635-1.88710.31041640.26421483X-RAY DIFFRACTION100
1.8871-1.91190.30711650.25071478X-RAY DIFFRACTION100
1.9119-1.93810.27251620.24291455X-RAY DIFFRACTION100
1.9381-1.96580.25171630.22991474X-RAY DIFFRACTION100
1.9658-1.99510.26451660.22161492X-RAY DIFFRACTION100
1.9951-2.02630.25331630.20441463X-RAY DIFFRACTION100
2.0263-2.05950.23831620.21061465X-RAY DIFFRACTION100
2.0595-2.09510.26391670.1991496X-RAY DIFFRACTION100
2.0951-2.13320.2411610.19431451X-RAY DIFFRACTION100
2.1332-2.17420.25371670.19381499X-RAY DIFFRACTION100
2.1742-2.21860.2381640.19581485X-RAY DIFFRACTION100
2.2186-2.26680.22821650.18141492X-RAY DIFFRACTION100
2.2668-2.31950.23151640.18441470X-RAY DIFFRACTION100
2.3195-2.37760.24121640.17971484X-RAY DIFFRACTION100
2.3776-2.44180.24681670.17961501X-RAY DIFFRACTION100
2.4418-2.51370.21671630.18261468X-RAY DIFFRACTION100
2.5137-2.59480.23811670.17641498X-RAY DIFFRACTION100
2.5948-2.68760.2531670.1841507X-RAY DIFFRACTION100
2.6876-2.79520.24251660.17741487X-RAY DIFFRACTION100
2.7952-2.92240.23231660.17851499X-RAY DIFFRACTION100
2.9224-3.07650.21751660.1791494X-RAY DIFFRACTION100
3.0765-3.26920.18121680.15181515X-RAY DIFFRACTION100
3.2692-3.52160.18821690.15821516X-RAY DIFFRACTION100
3.5216-3.8760.1931680.1591515X-RAY DIFFRACTION100
3.876-4.43680.17751700.14071524X-RAY DIFFRACTION100
4.4368-5.58940.2011730.14621564X-RAY DIFFRACTION100
5.5894-66.61430.2041820.18891629X-RAY DIFFRACTION100
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)
11.5442-0.29930.06851.7518-0.43312.0050.0144-0.0423-0.0356-0.014-0.0163-0.07540.07960.1237-0.00740.12790.00610.01630.1445-0.01520.1713-14.552414.3638-25.9853
21.77890.0527-0.18672.0611-0.16511.84350.0331-0.07640.08590.1316-0.0615-0.0316-0.03810.07710.01770.1935-0.00820.00880.1743-0.00040.1692-20.010740.7942-11.4603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 3:229)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 5:230)

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