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- PDB-1qwk: Structural genomics of Caenorhabditis Elegans: Hypothetical 35.2 ... -

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Basic information

Entry
Database: PDB / ID: 1qwk
TitleStructural genomics of Caenorhabditis Elegans: Hypothetical 35.2 kDa protein (aldose reductase family member)
Componentsaldo-keto reductase family 1 member C1
KeywordsOXIDOREDUCTASE / Structural genomics / Caenorhabditis Elegans / aldo-keto reductase / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


Glutathione conjugation / Estrogen biosynthesis / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Formation of xylulose-5-phosphate / RA biosynthesis pathway / Retinoid metabolism and transport / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / alcohol dehydrogenase (NADP+) activity ...Glutathione conjugation / Estrogen biosynthesis / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Formation of xylulose-5-phosphate / RA biosynthesis pathway / Retinoid metabolism and transport / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / alcohol dehydrogenase (NADP+) activity / aldose reductase (NADPH) activity / oxidoreductase activity / cytosol
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Aldo_ket_red domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChen, L. / Zhou, X.E. / Meehan, E.J. / Symersky, J. / Lu, S. / Li, S. / Luo, M. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Structural genomics of Caenorhabditis Elegans: Hypothetical 35.2 kDa protein (aldose reductase family member)
Authors: Chen, L. / Zhou, X.E. / Meehan, E.J. / Symersky, J. / Lu, S. / Li, S. / Luo, M.
History
DepositionSep 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aldo-keto reductase family 1 member C1


Theoretical massNumber of molelcules
Total (without water)35,2331
Polymers35,2331
Non-polymers00
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.050, 89.570, 116.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein aldo-keto reductase family 1 member C1 / Aldose reductase / XH961 / hypothetical protein C07D8.6 / Hypothetical 35.2 kDa protein


Mass: 35232.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: C07D8.6 / Plasmid: Pdest 17.1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P91020
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.18 Å3/Da / Density % sol: 43.2 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 41312 / Num. obs: 41312 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 12.3
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.243 / % possible all: 64.1

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Processing

Software
NameClassification
MAR345data collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AZ2

1az2


Resolution: 1.6→19.85 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1972 5 %RANDOM
Rwork0.2 ---
all0.201 39464 --
obs0.201 39464 87.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.4336 Å2 / ksol: 0.434452 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.06 Å20 Å20 Å2
2--15.65 Å20 Å2
3----9.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 0 330 2777
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 231 5.2 %
Rwork0.249 4176 -
obs-4176 59.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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