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- PDB-1o9j: The X-ray crystal structure of eta-crystallin -

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Basic information

Entry
Database: PDB / ID: 1o9j
TitleThe X-ray crystal structure of eta-crystallin
ComponentsALDEHYDE DEHYDROGENASE, CYTOSOLIC 1
KeywordsOXIDOREDUCTASE / ALDH / EYE-LENS PROTEIN / ETA-CRYSTALLIN
Function / homology
Function and homology information


ethanol catabolic process / aldehyde dehydrogenase (NAD+) / retinal metabolic process / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase (NAD+) activity / NAD binding / structural molecule activity / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase, cytosolic 1
Similarity search - Component
Biological speciesELEPHANTULUS EDWARDII (Cape elephant shrew)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPurkiss, A.G. / Van Montfort, R. / Wistow, G. / Slingsby, C.
CitationJournal: Biochemistry / Year: 2003
Title: Crystal Structure of Eta-Crystallin: Adaptation of a Class 1 Aldehyde Dehydrogenase for a New Role in the Eye Lens
Authors: Bateman, O.A. / Purkiss, A.G. / Van Montfort, R. / Slingsby, C. / Graham, C. / Wistow, G.
History
DepositionDec 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: ALDEHYDE DEHYDROGENASE, CYTOSOLIC 1
B: ALDEHYDE DEHYDROGENASE, CYTOSOLIC 1
C: ALDEHYDE DEHYDROGENASE, CYTOSOLIC 1
D: ALDEHYDE DEHYDROGENASE, CYTOSOLIC 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,36010
Polymers218,3974
Non-polymers2,9626
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.869, 136.407, 84.988
Angle α, β, γ (deg.)90.00, 102.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ALDEHYDE DEHYDROGENASE, CYTOSOLIC 1 / ETA-CRYSTALLIN / ALDH CLASS 1


Mass: 54599.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: NAD COFACTOR PRESENT
Source: (gene. exp.) ELEPHANTULUS EDWARDII (Cape elephant shrew)
Tissue: LENS / Organ: EYE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q28399, aldehyde dehydrogenase (NAD+)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMAJOR COMPONENT OF THE EYE OF ELEPHANT SHREWS. THIS ANIMAL HAS BOTH A LENS- AND A NON-LENS CLASS-1 ...MAJOR COMPONENT OF THE EYE OF ELEPHANT SHREWS. THIS ANIMAL HAS BOTH A LENS- AND A NON-LENS CLASS-1 ALDEHYDE DEHYDROGENASE 1.THE EYE-SPECIFIC FORM IS A STRUCTURAL PROTEIN OF THE LENS.

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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: 4.2 Å3/Da / Density % sol: 70.4 %
Crystal growpH: 6.5
Details: 25 MM BIS-TRIS-PROPANE PH 7.5, APPROXIMATELY 14% PEG 6,000.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mMBis-Tris-HCl1drop
21 mMEDTA1drop
31 mMdithiothreitol1droppH6.5
48 mg/mlprotein1drop
525 mMBis-Tris propane1reservoirpH7.5
614 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 15, 1999 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.4→45.6 Å / Num. obs: 67543 / % possible obs: 96.5 % / Observed criterion σ(I): 4 / Redundancy: 2.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 7.2 / % possible all: 94.7
Reflection
*PLUS
Num. measured all: 159192
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 94.7 % / Num. unique obs: 8412 / Num. measured obs: 20625

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BXS

1bxs


Resolution: 2.4→41.52 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.878 / SU B: 9.317 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 1.814 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3443 5.1 %RANDOM
Rwork0.18 ---
obs0.184 64100 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.32 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15139 0 192 454 15785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02215669
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214084
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.96721243
X-RAY DIFFRACTIONr_angle_other_deg0.817332960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16651972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.22364
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217360
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023000
X-RAY DIFFRACTIONr_nbd_refined0.1890.22921
X-RAY DIFFRACTIONr_nbd_other0.2150.215588
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.29304
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2419
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4271.59811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.828215775
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.34835858
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3454.55468
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 236
Rwork0.246 4609
Refinement
*PLUS
Num. reflection obs: 64099 / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.28

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