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- PDB-3d3w: Structure of L-Xylulose Reductase with bound coenzyme, phosphate ... -

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Basic information

Entry
Database: PDB / ID: 3d3w
TitleStructure of L-Xylulose Reductase with bound coenzyme, phosphate and hydroxide.
Components(L-xylulose reductase) x 2
KeywordsOXIDOREDUCTASE / L-Xylulose Reductase / Uronate Cycle / Short-Chain Dehydrogenase/Reductase(SDR) Superfamily / Glucose Metabolism / Acetylation / Carbohydrate metabolism / Membrane / NADP / Xylose metabolism
Function / homology
Function and homology information


Essential pentosuria / L-xylulose reductase / L-xylulose reductase (NADPH) activity / xylulose metabolic process / Formation of xylulose-5-phosphate / D-glucuronate catabolic process to D-xylulose 5-phosphate / carbonyl reductase (NADPH) activity / NADP metabolic process / D-xylose metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor ...Essential pentosuria / L-xylulose reductase / L-xylulose reductase (NADPH) activity / xylulose metabolic process / Formation of xylulose-5-phosphate / D-glucuronate catabolic process to D-xylulose 5-phosphate / carbonyl reductase (NADPH) activity / NADP metabolic process / D-xylose metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / cytoplasmic microtubule / brush border / microvillus / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHOSPHATE ION / L-xylulose reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsZhao, H.-T. / El-Kabbani, O.
CitationJournal: Cell.Mol.Life Sci. / Year: 2009
Title: Structure/function analysis of a critical disulfide bond in the active site of L-xylulose reductase.
Authors: Zhao, H.T. / Endo, S. / Ishikura, S. / Chung, R. / Hogg, P.J. / Hara, A. / El-Kabbani, O.
History
DepositionMay 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / 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 / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: L-xylulose reductase
B: L-xylulose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4805
Polymers51,8982
Non-polymers1,5823
Water10,034557
1
A: L-xylulose reductase
B: L-xylulose reductase
hetero molecules

A: L-xylulose reductase
B: L-xylulose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,96010
Polymers103,7964
Non-polymers3,1646
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area19130 Å2
ΔGint-137 kcal/mol
Surface area29920 Å2
MethodPISA
2
B: L-xylulose reductase
hetero molecules

A: L-xylulose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4805
Polymers51,8982
Non-polymers1,5823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5650 Å2
ΔGint-43 kcal/mol
Surface area18870 Å2
MethodPISA
3
A: L-xylulose reductase
hetero molecules

A: L-xylulose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4014
Polymers51,9142
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5870 Å2
ΔGint-36 kcal/mol
Surface area18480 Å2
MethodPISA
4
B: L-xylulose reductase
hetero molecules

B: L-xylulose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5596
Polymers51,8822
Non-polymers1,6774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6320 Å2
ΔGint-56 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.678, 87.476, 72.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 1 / Auth seq-ID: 1 - 244 / Label seq-ID: 1 - 244

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein L-xylulose reductase / XR / Dicarbonyl/L-xylulose reductase / Kidney dicarbonyl reductase / kiDCR / Carbonyl reductase II ...XR / Dicarbonyl/L-xylulose reductase / Kidney dicarbonyl reductase / kiDCR / Carbonyl reductase II / Sperm surface protein P34H


Mass: 25957.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CSO at position 138 / Source: (gene. exp.) Homo sapiens (human) / Gene: DCXR / Plasmid: pRset / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q7Z4W1, L-xylulose reductase
#2: Protein L-xylulose reductase / XR / Dicarbonyl/L-xylulose reductase / Kidney dicarbonyl reductase / kiDCR / Carbonyl reductase II ...XR / Dicarbonyl/L-xylulose reductase / Kidney dicarbonyl reductase / kiDCR / Carbonyl reductase II / Sperm surface protein P34H


Mass: 25941.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CYS/CSO at position 138 / Source: (gene. exp.) Homo sapiens (human) / Gene: DCXR / Plasmid: pRset / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q7Z4W1, L-xylulose reductase
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHERE IS MICROHETEROGENEITY IN THE RESIDUE IDENTITY CSO/CYS AT RESIDUE 138 IN CHAIN B AND THAT CYS ...THERE IS MICROHETEROGENEITY IN THE RESIDUE IDENTITY CSO/CYS AT RESIDUE 138 IN CHAIN B AND THAT CYS B 138 HAS A DOUBLE CONFORMATION AND FORMS A COVALENT BOND WITH A HYDROXIDE

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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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, POTASSIUM DIHYDROGENPHOSPHATE, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 31, 2007 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.87→30 Å / Num. all: 39016 / Num. obs: 37468 / % possible obs: 98.1 % / Redundancy: 5.04 % / Rmerge(I) obs: 0.0631 / Net I/σ(I): 12.6
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 5.64 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.3394

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.924 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25773 1932 5 %RANDOM
Rwork0.20403 ---
obs0.20678 36591 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.028 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.93 Å20 Å2
3----1.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.217 Å
Refinement stepCycle: LAST / Resolution: 1.87→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3663 0 101 557 4321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223827
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9985229
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7223.381139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14715622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1271530
X-RAY DIFFRACTIONr_chiral_restr0.110.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022786
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.22017
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22594
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3090.2371
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.2170
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.278
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.941.52511
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50223929
X-RAY DIFFRACTIONr_scbond_it2.27431495
X-RAY DIFFRACTIONr_scangle_it3.4434.51295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1820 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.10.05
tight thermal0.240.5
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 122 -
Rwork0.357 2602 -
obs--95.21 %

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