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

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Basic information

Entry
Database: PDB / ID: 4kge
TitleCrystal structure of near-infrared fluorescent protein with an extended stokes shift, pH 4.5
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)55,7025
Polymers55,5952
Non-polymers1063
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-51 kcal/mol
Surface area17920 Å2
MethodPISA
2
A: TagRFP675, red fluorescent protein
B: TagRFP675, red fluorescent protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)111,40310
Polymers111,1914
Non-polymers2136
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area12150 Å2
ΔGint-89 kcal/mol
Surface area32490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.050, 106.050, 219.526
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.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 3.2 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Na-acetate, pH 4.5, 3.0M NaCl, 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 27, 2009
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 32982 / % possible obs: 99.5 % / Redundancy: 21 % / Rmerge(I) obs: 0.09 / Χ2: 1.007 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3421.80.6616040.8991100
2.34-2.3821.70.55416030.8861100
2.38-2.4321.70.51216250.8951100
2.43-2.4821.80.44216300.9021100
2.48-2.5321.70.42416110.9311100
2.53-2.5921.80.34316440.9591100
2.59-2.6621.60.28716230.9761100
2.66-2.7321.70.22816131.0481100
2.73-2.8121.60.20516411.0061100
2.81-2.921.60.1716231.0681100
2.9-321.60.14516381.0941100
3-3.1221.50.11616641.331100
3.12-3.2621.50.09216320.9551100
3.26-3.4421.30.07616551.087199.9
3.44-3.6519.40.07115181.084191.1
3.65-3.9318.90.0716491.104198.7
3.93-4.3320.60.06116800.9631100
4.33-4.9520.10.05717070.915199.9
4.95-6.2419.50.04517451.0681100
6.24-5018.90.03418770.987199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.23 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.11 Å
Translation2.5 Å47.11 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BXA

3bxa


Resolution: 2.3→47.11 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2287 / WRfactor Rwork: 0.1842 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8617 / SU B: 7.799 / SU ML: 0.105 / SU R Cruickshank DPI: 0.0466 / SU Rfree: 0.0408 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 1654 5 %RANDOM
Rwork0.1877 ---
obs0.1899 32794 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.06 Å2 / Biso mean: 40.5447 Å2 / Biso min: 17.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 3 242 3813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193737
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9735056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60624.244172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9415655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5281519
X-RAY DIFFRACTIONr_chiral_restr0.0860.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212860
LS refinement shellResolution: 2.303→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 109 -
Rwork0.208 2234 -
all-2343 -
obs--99.49 %
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)
10.8489-0.0296-0.07120.9019-0.23971.216-0.01840.1181-0.0884-0.0698-0.06860.020.2237-0.1020.0870.0505-0.04330.03220.1137-0.07020.0559-10.002734.62465.0268
21.44750.0667-0.93350.7337-0.45672.0656-0.0164-0.2433-0.05390.1196-0.13-0.047-0.04680.42430.14640.0464-0.0474-0.0320.13250.06240.0366-13.987637.422835.7981
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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