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- PDB-9lm8: Crystal structure of bvFP-Pfr21 -

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Basic information

Entry
Database: PDB / ID: 9lm8
TitleCrystal structure of bvFP-Pfr21
ComponentsbvFP-Pfr21
KeywordsDE NOVO PROTEIN / Near-infrared protein
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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-Pfr21


Theoretical massNumber of molelcules
Total (without water)42,8791
Polymers42,8791
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.625, 45.576, 59.021
Angle α, β, γ (deg.)102.75, 102.06, 102.21
Int Tables number1
Space group name H-MP1

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Components

#1: Protein bvFP-Pfr21


Mass: 42878.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 10% v/v 2-propanol; 0.1 M sodium citrate tribasic dihydrate (pH 5.0); and 26% v/v polyethylene glycol 400
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: 2.45→42.8 Å / Num. obs: 14135 / % possible obs: 88.23 % / Redundancy: 3.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.121 / Net I/σ(I): 6.6
Reflection shellResolution: 2.45→2.538 Å / Num. unique obs: 7175 / CC1/2: 0.84

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
PHENIXphasing
autoPROCdata processing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→42.8 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 1299 10.03 %
Rwork0.2378 --
obs0.2429 12954 88.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 0 37 3054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.56
X-RAY DIFFRACTIONf_dihedral_angle_d4.664437
X-RAY DIFFRACTIONf_chiral_restr0.033476
X-RAY DIFFRACTIONf_plane_restr0.005537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.550.30921450.25921220X-RAY DIFFRACTION84
2.55-2.660.32981380.2511228X-RAY DIFFRACTION84
2.66-2.80.2751410.25361265X-RAY DIFFRACTION86
2.8-2.980.31571470.26641313X-RAY DIFFRACTION89
2.98-3.210.30951410.25071337X-RAY DIFFRACTION91
3.21-3.530.29881470.2471322X-RAY DIFFRACTION90
3.53-4.040.27461460.22171305X-RAY DIFFRACTION89
4.04-5.090.27461490.21541340X-RAY DIFFRACTION90
5.09-42.80.26311450.23231325X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 4.6152 Å / Origin y: -24.632 Å / Origin z: 18.8108 Å
111213212223313233
T0.1475 Å20.0045 Å2-0.116 Å2-0.2273 Å2-0.0195 Å2--0.2481 Å2
L1.5689 °2-0.7524 °2-0.6485 °2-1.7011 °20.3144 °2--1.0623 °2
S-0.1155 Å °0.1663 Å °-0.1765 Å °-0.2036 Å °-0.0396 Å °0.2295 Å °0.205 Å °0.0284 Å °0.0803 Å °
Refinement TLS groupSelection details: all

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