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- PDB-3qk3: Crystal structure of human beta-crystallin B3 -

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Basic information

Entry
Database: PDB / ID: 3qk3
TitleCrystal structure of human beta-crystallin B3
ComponentsBeta-crystallin B3
KeywordsSTRUCTURAL PROTEIN / CRYBB3 / crystallin / beta B3 / cataract / eye lens protein / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception
Similarity search - Function
Crystallins / Gamma-B Crystallin; domain 1 / Beta/Gamma crystallin / : / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKrojer, T. / Gileadi, C. / Cocking, R. / Muniz, J. / Pilka, E. / Yue, W.W. / Vollmar, M. / Pike, A.C.W. / von Delft, F. / Bountra, C. ...Krojer, T. / Gileadi, C. / Cocking, R. / Muniz, J. / Pilka, E. / Yue, W.W. / Vollmar, M. / Pike, A.C.W. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Kavanagh, K. / Oppermann, U. / Structural Genomics Consortium (SGC)
History
DepositionJan 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-crystallin B3
B: Beta-crystallin B3
C: Beta-crystallin B3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,14913
Polymers64,3583
Non-polymers79110
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-59 kcal/mol
Surface area21880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.778, 82.627, 63.592
Angle α, β, γ (deg.)90.00, 97.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-crystallin B3 / Beta-B3 crystallin


Mass: 21452.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYBB3, CRYB3 / Production host: Escherichia coli (E. coli) / References: UniProt: P26998
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 1.5M Li2SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.95→19.63 Å / Num. all: 35273 / Num. obs: 35273 / % possible obs: 95.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 24.34 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.5
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5073 / % possible all: 94.9

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OKI

1oki


Resolution: 1.95→19.63 Å / Cor.coef. Fo:Fc: 0.9544 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1760 4.99 %RANDOM
Rwork0.1717 ---
all0.1734 35273 --
obs0.1734 35273 --
Displacement parametersBiso mean: 28.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.0486 Å20 Å2-1.2127 Å2
2--0.7259 Å20 Å2
3----1.7745 Å2
Refine analyzeLuzzati coordinate error obs: 0.231 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 45 315 4660
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0145172
X-RAY DIFFRACTIONt_angle_deg0.9861262
X-RAY DIFFRACTIONt_dihedral_angle_d20442
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1162
X-RAY DIFFRACTIONt_gen_planes6655
X-RAY DIFFRACTIONt_it451720
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.83
X-RAY DIFFRACTIONt_other_torsion2.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion5225
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact54134
LS refinement shellResolution: 1.95→2.01 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2311 134 4.7 %
Rwork0.2183 2718 -
all0.219 2852 -
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)
12.17661.0615-0.40421.87030.57561.0610.0367-0.2245-0.10780.2526-0.0191-0.07310.04010.0977-0.0177-0.03860.0025-0.0153-0.06170.0042-0.025910.94961.764142.1337
20.4728-0.2674-1.13591.30060.9519-0.2495-0.00720.05750.01770.05240.00870.0241-0.0161-0.0319-0.00150.04280.04610.1156-0.03850.07560.15387.051316.613325.7519
31.78620.6385-0.10012.04920.37731.42310.09070.05210.06970.03860.0374-0.0286-0.11040.0818-0.1281-0.0224-0.01870.039-0.0683-0.0173-0.007823.483413.182325.1288
42.2448-0.0853-0.58242.3134-0.57542.4480.01330.1574-0.0694-0.08660.04370.03890.2111-0.2043-0.057-0.0541-0.0087-0.0291-0.05930.0061-0.047310.504830.676343.1529
50.19470.09640.59220-1.01591.54570.0133-0.03710.0018-0.00390.02770.02930.0405-0.0497-0.0410.01030.02960.00560.1434-0.0656-0.005127.20540.742656.4574
61.70710.5104-0.32621.2437-0.13241.61450.0627-0.1859-0.06890.006-0.0052-0.1064-0.03940.0524-0.0575-0.02770.00570.0016-0.02840.0001-0.025434.553233.623543.3751
75.37690.44961.12771.8609-0.08713.5533-0.1076-0.22240.47750.1210.06120.3008-0.4337-0.11130.0464-0.03850.04440.0072-0.0855-0.014-0.093724.448815.9663.9223
80.46561.445-0.06230.76261.8262-0.0263-0.0093-0.0411-0.0185-0.01250.0008-0.0004-0.0153-0.04420.00850.0009-0.047-0.0696-0.0429-0.15080.194328.0344-5.377557.9329
93.555-0.80810.53931.2206-0.26431.77470.07920.5501-0.4031-0.0777-0.16810.13690.0767-0.00430.0889-0.13810.0126-0.00340.1284-0.0784-0.112838.73523.267649.182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 23:107)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 108:114)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 115:198)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 23:107)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 108:114)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 115:198)
7X-RAY DIFFRACTION7(CHAIN C AND RESID 23:107)
8X-RAY DIFFRACTION8(CHAIN C AND RESID 108:114)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 115:198)

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