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- PDB-9d1v: Human Beta-B2 Crystallin -

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Basic information

Entry
Database: PDB / ID: 9d1v
TitleHuman Beta-B2 Crystallin
ComponentsBeta-crystallin B2
KeywordsSTRUCTURAL PROTEIN / Eye lens / oligomerisation / cataracts
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception / structural molecule activity / identical protein binding
Similarity search - Function
Beta/Gamma crystallin / : / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Beta-crystallin B2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFrkic, R.L. / Jackson, C.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: To Be Published
Title: Human Beta-B2 Crystallin
Authors: Frkic, R.L. / Jackson, C.J.
History
DepositionAug 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-crystallin B2
B: Beta-crystallin B2
C: Beta-crystallin B2
D: Beta-crystallin B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8136
Polymers93,6484
Non-polymers1652
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13960 Å2
ΔGint-26 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.491, 82.915, 153.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Beta-crystallin B2 / Beta-B2 crystallin / Beta-crystallin Bp


Mass: 23411.932 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYBB2, CRYB2, CRYB2A / Production host: Escherichia coli (E. coli) / References: UniProt: P43320
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.05 Å3/Da / Density % sol: 40.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 3350, 0.3 M Potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→48.87 Å / Num. obs: 52335 / % possible obs: 99.1 % / Redundancy: 27.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.042 / Rrim(I) all: 0.222 / Χ2: 1.04 / Net I/σ(I): 11.5 / Num. measured all: 1433206
Reflection shellResolution: 2→2.05 Å / % possible obs: 98.3 % / Redundancy: 28.8 % / Rmerge(I) obs: 5.63 / Num. measured all: 108585 / Num. unique obs: 3774 / CC1/2: 0.675 / Rpim(I) all: 1.057 / Rrim(I) all: 5.729 / Χ2: 1.04 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.87 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 2526 4.85 %
Rwork0.2187 --
obs0.2208 52097 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5986 0 11 227 6224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.454
X-RAY DIFFRACTIONf_dihedral_angle_d4.131811
X-RAY DIFFRACTIONf_chiral_restr0.048821
X-RAY DIFFRACTIONf_plane_restr0.0031110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.37631280.34962688X-RAY DIFFRACTION98
2.04-2.080.40961260.35132729X-RAY DIFFRACTION97
2.08-2.130.38651300.34122687X-RAY DIFFRACTION97
2.13-2.170.33061470.33262656X-RAY DIFFRACTION98
2.17-2.230.3371340.32022733X-RAY DIFFRACTION98
2.23-2.290.43171410.34422680X-RAY DIFFRACTION98
2.29-2.360.37321310.2942726X-RAY DIFFRACTION98
2.36-2.430.38451480.30272723X-RAY DIFFRACTION98
2.43-2.520.37871140.27952757X-RAY DIFFRACTION98
2.52-2.620.30481430.28122717X-RAY DIFFRACTION99
2.62-2.740.31121660.27542712X-RAY DIFFRACTION98
2.74-2.880.33691390.27382749X-RAY DIFFRACTION99
2.88-3.070.35121440.2432757X-RAY DIFFRACTION99
3.07-3.30.26271530.22052776X-RAY DIFFRACTION99
3.3-3.630.23931380.20252798X-RAY DIFFRACTION99
3.63-4.160.21631470.17172829X-RAY DIFFRACTION99
4.16-5.240.1871480.15072859X-RAY DIFFRACTION100
5.24-48.870.21761490.18142995X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.36090.2629-0.63354.00522.36576.3546-0.03620.09690.0392-0.38040.0857-0.0814-0.44220.3953-0.04830.35970.00110.01620.54450.01390.2538-0.0156-1.2033-55.3391
22.0739-0.2309-0.59923.7357-0.02943.973-0.17680.0163-0.34890.01520.0548-0.35230.77620.85360.13320.4650.14790.05330.6209-0.03170.329-3.9596-0.5872-14.2962
32.67890.8635-0.26668.4892-0.71583.6593-0.30010.26330.1064-0.64950.16730.4841-0.3704-1.14010.11910.53230.1677-0.0850.8738-0.15360.3623-32.861.3021-58.3009
40.98870.70610.34931.37-0.14425.25750.04770.1991-0.06130.0205-0.39130.246-0.0083-0.97340.37520.4930.11020.03060.7932-0.12130.4098-28.7697-4.2231-52.8892
52.7052-0.49730.64614.20220.45014.2582-0.11640.0919-0.0815-0.1834-0.12210.25460.472-0.5180.24850.3408-0.09480.0570.5313-0.07070.2822-29.91784.1585-14.8803
64.02752.6665-5.82627.3799-2.82359.03050.0627-0.35090.77820.29250.24580.2256-0.55210.0176-0.16760.3199-0.0288-0.07460.6352-0.06720.3942-16.058923.6353-4.3951
73.40110.14680.23063.8290.22441.94320.0362-0.69520.01340.35660.0494-0.2185-0.07030.7529-0.09010.279-0.0234-0.0180.605-0.02230.2602-9.939314.544-4.234
84.47611.10571.18183.25011.79283.8981-0.2074-0.40610.6055-0.2566-0.09980.2681-1.0926-0.31410.26590.7060.0993-0.040.462-0.05210.3283-15.232613.961-45.0206
93.9974-1.7778-1.60436.17911.26112.87170.17640.6080.0721-0.0149-0.23610.1101-0.94580.64550.15960.7402-0.08370.0070.6351-0.0730.2883-8.14889.2384-46.9743
105.9124-0.50780.98952.5128-1.09512.5314-0.1379-0.8434-0.73210.1938-0.1339-0.17651.6822-0.27470.28931.3644-0.13140.18150.66050.07530.4891-22.0019-17.6675-0.8497
112.4306-0.1631-1.35352.0587-0.05766.1344-0.0263-0.3776-0.16440.4935-0.10720.14440.9406-0.57450.14540.8501-0.08480.09550.5214-0.01040.3822-24.2658-7.7443-4.847
123.78561.0499-0.94134.2317-0.83233.0331-0.0375-0.1665-0.36750.2577-0.217-0.0630.5841-0.3270.25210.5515-0.00450.03150.5169-0.07970.267-17.1969-14.947-44.9711
134.9931-1.6217-2.29554.6177-0.71466.72230.0826-0.33660.65150.18580.12320.3294-0.3058-1.6805-0.12640.5824-0.05240.00810.8252-0.10020.3607-27.648-1.752-41.6301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 106 )
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 200 )
3X-RAY DIFFRACTION3chain 'B' and (resid 13 through 83 )
4X-RAY DIFFRACTION4chain 'B' and (resid 84 through 106 )
5X-RAY DIFFRACTION5chain 'B' and (resid 107 through 195 )
6X-RAY DIFFRACTION6chain 'C' and (resid 12 through 33 )
7X-RAY DIFFRACTION7chain 'C' and (resid 34 through 106 )
8X-RAY DIFFRACTION8chain 'C' and (resid 107 through 170 )
9X-RAY DIFFRACTION9chain 'C' and (resid 171 through 196 )
10X-RAY DIFFRACTION10chain 'D' and (resid 14 through 61 )
11X-RAY DIFFRACTION11chain 'D' and (resid 62 through 106 )
12X-RAY DIFFRACTION12chain 'D' and (resid 107 through 184 )
13X-RAY DIFFRACTION13chain 'D' and (resid 185 through 195 )

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