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- PDB-3f3s: The Crystal Structure of Human Lambda-Crystallin, CRYL1 -

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Basic information

Entry
Database: PDB / ID: 3f3s
TitleThe Crystal Structure of Human Lambda-Crystallin, CRYL1
ComponentsLambda-crystallin homolog
KeywordsSTRUCTURAL PROTEIN / CRYL1 / lambda-crystallin / Crystallin / lambda 1 / CRY / GDH / L-gulonate 3-dehydrogenase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


L-gulonate 3-dehydrogenase / L-gulonate 3-dehydrogenase activity / glucuronate catabolic process to xylulose 5-phosphate / Formation of xylulose-5-phosphate / 3-hydroxyacyl-CoA dehydrogenase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD+ binding / fatty acid metabolic process / protein homodimerization activity / extracellular exosome / cytosol
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Lambda-crystallin homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsUgochukwu, E. / Johansson, C. / Yue, W.W. / Kochan, G. / Pilka, E. / Kramm, A. / Pike, A.C.W. / Filippakopoulos, P. / von Delft, F. / Bountra, C. ...Ugochukwu, E. / Johansson, C. / Yue, W.W. / Kochan, G. / Pilka, E. / Kramm, A. / Pike, A.C.W. / Filippakopoulos, P. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Human Lambda-Crystallin, CRYL1
Authors: Ugochukwu, E. / Johansson, C. / Yue, W.W. / Kochan, G. / Pilka, E. / Kramm, A. / Pike, A.C.W. / Filippakopoulos, P. / von Delft, F. / Oppermann, U.
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Lambda-crystallin homolog
B: Lambda-crystallin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,97416
Polymers69,7532
Non-polymers2,22114
Water5,981332
1
A: Lambda-crystallin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9527
Polymers34,8771
Non-polymers1,0756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lambda-crystallin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0239
Polymers34,8771
Non-polymers1,1468
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14940 Å2
ΔGint-216 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.085, 102.085, 134.986
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lambda-crystallin homolog / CRYL1


Mass: 34876.570 Da / Num. of mol.: 2 / Fragment: residues 6-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYL1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: Q9Y2S2

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Non-polymers , 5 types, 346 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99987 Å
DetectorType: MAR225 / Detector: CCD / Date: Oct 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2→47.73 Å / Num. obs: 53793 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.297 / Mean I/σ(I) obs: 2.5 / Num. unique all: 69408 / Rsym value: 1.297 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0055refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DPO

2dpo
PDB Unreleased entry


Resolution: 2→47.73 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.921 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.132 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19629 2731 5.1 %RANDOM
Rwork0.15447 ---
all0.15654 51002 --
obs0.15654 51002 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.408 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å2-0.53 Å20 Å2
2---1.06 Å20 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 2→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4754 0 136 332 5222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225025
X-RAY DIFFRACTIONr_bond_other_d0.0010.023393
X-RAY DIFFRACTIONr_angle_refined_deg1.4632.0096833
X-RAY DIFFRACTIONr_angle_other_deg0.913.0028298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3525641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84124.392189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40415876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9811527
X-RAY DIFFRACTIONr_chiral_restr0.0860.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02907
X-RAY DIFFRACTIONr_mcbond_it3.92653139
X-RAY DIFFRACTIONr_mcbond_other1.65251260
X-RAY DIFFRACTIONr_mcangle_it4.95575081
X-RAY DIFFRACTIONr_scbond_it7.41491886
X-RAY DIFFRACTIONr_scangle_it9.386111742
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 209 -
Rwork0.225 3724 -
obs--99.92 %
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)
13.6581-0.91840.12855.74681.2192.5681-0.11640.31620.108-0.21070.1935-0.3541-0.16740.2831-0.077-0.0178-0.0896-0.00140.0071-0.0147-0.1428-19.26714.089-14.055
223.700311.6537-8.79613.7479000.58551.4017-0.1825-1.1753-0.2904-0.04040.11090.4314-0.29510.189-0.1313-0.02330.1839-0.0374-0.0868-23.37214.689-26.223
32.11560.3580.58881.75480.1452.4537-0.0960.12380.0057-0.01960.1246-0.2033-0.04820.2436-0.0285-0.0272-0.0351-0.0324-0.1011-0.0374-0.1059-23.21914.266-4.743
41.8036-0.1549-0.1181.3314-0.1481.3614-0.02890.1399-0.0392-0.02590.01910.1807-0.0226-0.02220.0099-0.06850.0151-0.0052-0.10460.0113-0.057-49.385.378-9.377
50.8699-0.68180.28024.9651-3.17384.24-0.0936-0.03390.02810.11270.18580.5832-0.2165-0.2521-0.0922-0.07780.0525-0.0326-0.02290.08690.281-76.04421.442-12.978
64.46971.0092-0.21293.7735-1.75882.96360.00170.1793-0.3077-0.23920.28220.76020.2772-0.3903-0.2839-0.047-0.0079-0.0812-0.06450.08760.2687-74.0985.477-12.867
72.3212-0.20020.59721.915-0.45751.2554-0.0409-0.14310.03260.1870.03020.1377-0.11190.03280.0106-0.04880.01560.0092-0.13630.0141-0.0891-47.7985.921-2.583
83.6886-1.6042-1.79637.71896.121214.0997-0.0468-0.04910.56930.03550.02830.2774-0.91830.03060.01860.05130.004-0.0825-0.12890.05230.2015-54.7124.907-10.028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 42
2X-RAY DIFFRACTION2A43 - 58
3X-RAY DIFFRACTION3A59 - 184
4X-RAY DIFFRACTION4A185 - 316
5X-RAY DIFFRACTION5B6 - 104
6X-RAY DIFFRACTION6B105 - 187
7X-RAY DIFFRACTION7B188 - 283
8X-RAY DIFFRACTION8B284 - 316

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