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- PDB-4kgf: Crystal structure of near-infrared fluorescent protein with an ex... -

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Basic information

Entry
Database: PDB / ID: 4kgf
TitleCrystal structure of near-infrared fluorescent protein with an extended stokes shift, ph 8.0
ComponentsTagRFP675, red fluorescent protein
KeywordsFLUORESCENT PROTEIN / STRUCTURAL GENOMICS / PROTEINSTRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCHCONSORTIUM / HYDROLASE / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsMalashkevich, V.N. / Piatkevich, K. / Almo, S.C. / Verkhusha, V. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: Sci Rep / Year: 2013
Title: Extended Stokes shift in fluorescent proteins: chromophore-protein interactions in a near-infrared TagRFP675 variant.
Authors: Piatkevich, K.D. / Malashkevich, V.N. / Morozova, K.S. / Nemkovich, N.A. / Almo, S.C. / Verkhusha, V.V.
History
DepositionApr 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TagRFP675, red fluorescent protein
B: TagRFP675, red fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6313
Polymers55,5952
Non-polymers351
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-31 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.893, 105.893, 217.982
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Detailsdimeric

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Components

#1: Protein TagRFP675, red fluorescent protein


Mass: 27797.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: PBAD/HIS-B / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 3.17 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Na-acetate, pH 4.5, 3.0M NaCl. Then Solution slowly replaced with 0.1M Tris-HCl, pH 8.0, 3.0M NaCl 8-10 min, color change (darker), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2009
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 35919 / % possible obs: 99.2 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.074 / Χ2: 1.302 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.23-2.2714.10.92115250.791186.2
2.27-2.3115.70.74417700.8281100
2.31-2.3515.90.60217790.8051100
2.35-2.4160.5417520.8081100
2.4-2.4515.90.45117850.8441100
2.45-2.5115.90.43817610.8471100
2.51-2.5715.90.32517770.8661100
2.57-2.6415.90.28317750.8981100
2.64-2.7215.90.20717860.9351100
2.72-2.8115.90.18417760.977199.9
2.81-2.9115.90.14517850.9881100
2.91-3.0315.80.12217971.0311100
3.03-3.1615.70.08918071.1241100
3.16-3.3315.70.06817961.246199.9
3.33-3.5415.60.05618191.472199.9
3.54-3.8115.60.05418191.718199.8
3.81-4.215.40.05718332.4841100
4.2-4.815.10.05718453.397199.6
4.8-6.0514.60.04518932.1441100
6.05-5013.80.03420391.769199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KGE

4kge


Resolution: 2.3→46.85 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 9.491 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1650 5 %RANDOM
Rwork0.1911 ---
obs0.1932 32806 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.45 Å2 / Biso mean: 56.2677 Å2 / Biso min: 25.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0 Å2-0 Å2
2---0.3 Å2-0 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 1 192 3749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193705
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9745008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5575451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29724.176170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13815651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9851520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212831
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 122 -
Rwork0.189 2201 -
all-2323 -
obs--99.79 %
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)
11.1887-0.1358-0.61731.2309-0.21942.3518-0.01190.3097-0.1358-0.0665-0.1510.01030.3697-0.35030.16290.0695-0.0530.02520.1926-0.09560.1419-10.044934.97874.5048
21.69420.2163-1.73530.7421-0.8433.77030.0008-0.2886-0.11450.1716-0.1787-0.0954-0.19630.56610.1780.0634-0.0632-0.06740.12070.0910.1286-13.793637.126635.3898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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