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- PDB-9lm9: Crystal structure of bvFP-Pfr21 -

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Basic information

Entry
Database: PDB / ID: 9lm9
TitleCrystal structure of bvFP-Pfr21
ComponentsbvFP-Pfr16.v14
KeywordsDE NOVO PROTEIN / Near-infrared protein
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsDing, G. / Xu, Z. / Cao, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: De novo design of NIR-I/II fluorescent proteins for in vivo deep tissue imaging
Authors: Ding, G. / Xu, Z. / Cao, L.
History
DepositionJan 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: bvFP-Pfr16.v14
B: bvFP-Pfr16.v14


Theoretical massNumber of molelcules
Total (without water)85,8102
Polymers85,8102
Non-polymers00
Water00
1
A: bvFP-Pfr16.v14


Theoretical massNumber of molelcules
Total (without water)42,9051
Polymers42,9051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: bvFP-Pfr16.v14


Theoretical massNumber of molelcules
Total (without water)42,9051
Polymers42,9051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.320, 77.000, 86.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein bvFP-Pfr16.v14


Mass: 42904.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 10% (w/v) PEG 8000; 100mM imidazole/Hydrochloric acid pH 8.0
PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.24→46.62 Å / Num. obs: 16978 / % possible obs: 96.9 % / Redundancy: 3.2 % / CC1/2: 0.996 / Net I/σ(I): 7.6
Reflection shellResolution: 3.24→3.32 Å / Num. unique obs: 1277 / CC1/2: 0.55

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
PHENIXphasing
xia2data scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.24→46.62 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3668 1694 10.01 %
Rwork0.3193 --
obs0.324 16925 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.24→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5600 0 0 0 5600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.647
X-RAY DIFFRACTIONf_dihedral_angle_d18.812846
X-RAY DIFFRACTIONf_chiral_restr0.038916
X-RAY DIFFRACTIONf_plane_restr0.0071015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.340.41731440.3841299X-RAY DIFFRACTION99
3.34-3.440.41221410.39451267X-RAY DIFFRACTION99
3.44-3.570.41861420.36241270X-RAY DIFFRACTION99
3.57-3.710.42141410.35991280X-RAY DIFFRACTION98
3.71-3.880.37861390.35041252X-RAY DIFFRACTION97
3.88-4.080.36311380.34161235X-RAY DIFFRACTION96
4.08-4.340.41241400.33741256X-RAY DIFFRACTION96
4.34-4.670.40591400.32661267X-RAY DIFFRACTION97
4.67-5.140.41091460.31521304X-RAY DIFFRACTION99
5.14-5.880.43481440.37231299X-RAY DIFFRACTION97
5.89-7.410.46121340.3541204X-RAY DIFFRACTION90
7.42-46.620.23591450.21341298X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -31.3218 Å / Origin y: 19.6439 Å / Origin z: -0.2475 Å
111213212223313233
T0.387 Å2-0.069 Å2-0.1406 Å2-0.6261 Å2-0.0513 Å2--0.3921 Å2
L5.8424 °2-0.4719 °2-0.6967 °2-1.1467 °20.0218 °2--0.9252 °2
S-0.0894 Å °-0.3597 Å °0.1354 Å °0.0679 Å °0.0762 Å °-0.1622 Å °0.0183 Å °0.4419 Å °0.0377 Å °
Refinement TLS groupSelection details: all

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