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- PDB-9lm7: Crystal structrue of bvFP-Pr1-88.4 -

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Basic information

Entry
Database: PDB / ID: 9lm7
TitleCrystal structrue of bvFP-Pr1-88.4
ComponentsbvFP-Pr1-88.4
KeywordsDE NOVO PROTEIN / Near-infrared protein
Function / homologyBILIVERDINE IX ALPHA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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-Pr1-88.4
B: bvFP-Pr1-88.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3324
Polymers84,1662
Non-polymers1,1652
Water14,952830
1
A: bvFP-Pr1-88.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6662
Polymers42,0831
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: bvFP-Pr1-88.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6662
Polymers42,0831
Non-polymers5831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.921, 81.656, 84.443
Angle α, β, γ (deg.)90.00, 95.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein bvFP-Pr1-88.4


Mass: 42083.238 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)
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 1.1 M ammonium tartrate dibasic (pH 7.0), 10% v/v 2-propanol
PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→29.28 Å / Num. obs: 96135 / % possible obs: 99.57 % / Redundancy: 3.2 % / CC1/2: 1 / Net I/σ(I): 37.08
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 9419 / CC1/2: 0.966

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PHENIXphasing
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.28 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 1993 2.08 %
Rwork0.1976 --
obs0.1981 95987 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5905 0 0 830 6735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075950
X-RAY DIFFRACTIONf_angle_d1.018011
X-RAY DIFFRACTIONf_dihedral_angle_d7.261865
X-RAY DIFFRACTIONf_chiral_restr0.051940
X-RAY DIFFRACTIONf_plane_restr0.011030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.36631370.3076462X-RAY DIFFRACTION97
1.85-1.890.32091420.27976701X-RAY DIFFRACTION99
1.89-1.950.28331390.23976673X-RAY DIFFRACTION99
1.95-2.010.28061420.23086663X-RAY DIFFRACTION100
2.01-2.090.25031420.21586713X-RAY DIFFRACTION100
2.09-2.170.231430.20946708X-RAY DIFFRACTION100
2.17-2.270.21991430.19076744X-RAY DIFFRACTION100
2.27-2.390.22431430.19756693X-RAY DIFFRACTION100
2.39-2.540.20951430.20026733X-RAY DIFFRACTION100
2.54-2.730.23491430.19566769X-RAY DIFFRACTION100
2.73-3.010.22531430.19916753X-RAY DIFFRACTION100
3.01-3.440.21751440.18496732X-RAY DIFFRACTION100
3.44-4.330.17421440.17096774X-RAY DIFFRACTION100
4.33-29.280.2081450.18986876X-RAY DIFFRACTION100

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