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- PDB-3nt9: CRYSTAL STRUCTURE OF LSSmKate1 red fluorescent proteins with larg... -

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Basic information

Entry
Database: PDB / ID: 3nt9
TitleCRYSTAL STRUCTURE OF LSSmKate1 red fluorescent proteins with large Stokes shift
ComponentsLSSmKate1 red fluorescent protein
KeywordsFLUORESCENT PROTEIN / red fluorescent protein / large Stokes shift
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesArtificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å
AuthorsMalashkevich, V.N. / Piatkevich, K. / Almo, S.C. / Verkhusha, V.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Engineering ESPT Pathways Based on Structural Analysis of LSSmKate Red Fluorescent Proteins with Large Stokes Shift.
Authors: Piatkevich, K.D. / Malashkevich, V.N. / Almo, S.C. / Verkhusha, V.V.
History
DepositionJul 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LSSmKate1 red fluorescent protein
B: LSSmKate1 red fluorescent protein
C: LSSmKate1 red fluorescent protein
D: LSSmKate1 red fluorescent protein


Theoretical massNumber of molelcules
Total (without water)110,5134
Polymers110,5134
Non-polymers00
Water7,873437
1
A: LSSmKate1 red fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,6281
Polymers27,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LSSmKate1 red fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,6281
Polymers27,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LSSmKate1 red fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,6281
Polymers27,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: LSSmKate1 red fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,6281
Polymers27,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: LSSmKate1 red fluorescent protein
B: LSSmKate1 red fluorescent protein


Theoretical massNumber of molelcules
Total (without water)55,2572
Polymers55,2572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-22 kcal/mol
Surface area17940 Å2
MethodPISA
6
C: LSSmKate1 red fluorescent protein
D: LSSmKate1 red fluorescent protein


Theoretical massNumber of molelcules
Total (without water)55,2572
Polymers55,2572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-20 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.177, 72.177, 226.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsAUTHOR STATES THAT IT IS MONOMER IN SOLUTION.

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Components

#1: Protein
LSSmKate1 red fluorescent protein


Mass: 27628.342 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artificial gene (others) / Plasmid: pBAD/His-B / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG 1000, 0.1 M phosphate-citrate, pH 5.6, 0.2 M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 76485 / % possible obs: 96.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.99-2.024.10.71766.8
2.02-2.064.80.59684.7
2.06-2.15.20.56990.8
2.1-2.145.70.52695.1
2.14-2.196.10.47198.1
2.19-2.246.30.41399.4
2.24-2.36.70.34199.8
2.3-2.366.90.315100
2.36-2.437.10.256100
2.43-2.517.10.212100
2.51-2.67.20.177100
2.6-2.77.30.14100
2.7-2.827.30.12100
2.82-2.977.40.1100
2.97-3.167.40.082100
3.16-3.47.40.066100
3.4-3.747.40.061100
3.74-4.297.30.055100
4.29-5.47.10.04199.9
5.4-507.50.03499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.9 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.56 Å
Translation2.5 Å32.56 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.2phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→19.81 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.182 / SU ML: 0.113 / SU R Cruickshank DPI: 0.1594 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23179 3843 5 %RANDOM
Rwork0.18215 ---
obs0.18463 72452 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.744 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.99→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7148 0 0 437 7585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227374
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.9769953
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2435892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72424.256336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.957151278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3361537
X-RAY DIFFRACTIONr_chiral_restr0.1140.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215625
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0943.54428
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.031507140
X-RAY DIFFRACTIONr_scbond_it8.887502946
X-RAY DIFFRACTIONr_scangle_it1.4134.52813
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.994→2.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 233 -
Rwork0.3 4302 -
obs--79.46 %
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)
11.4852-0.1610.01311.68170.34561.1017-0.02560.129-0.1485-0.07790.0663-0.19740.03860.033-0.04060.0252-0.00040.01990.0986-0.02380.044923.110415.593819.9482
21.5318-0.1145-0.15711.70440.28421.021-0.0365-0.12160.28330.07080.0063-0.0856-0.0755-0.04430.03020.04630.0065-0.02360.0696-0.03340.062612.942640.404233.5578
32.6641-0.13080.12761.31440.04510.6412-0.06450.12540.41840.0279-0.06220.2488-0.0264-0.06430.12660.00960.0023-0.01690.13310.00290.1464-16.618931.31226.3609
42.0613-0.3632-0.07421.7824-0.03580.9246-0.00170.325-0.5402-0.109-0.03980.24410.112-0.11260.04150.0313-0.0271-0.01080.1492-0.08670.1578-6.08634.032719.0933
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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