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- PDB-1pr9: Human L-Xylulose Reductase Holoenzyme -

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Basic information

Entry
Database: PDB / ID: 1pr9
TitleHuman L-Xylulose Reductase Holoenzyme
ComponentsL-XYLULOSE REDUCTASE
KeywordsOXIDOREDUCTASE / short chain dehydrogenase/reductase / dinucleotide binding domain
Function / homology
Function and homology information


Essential pentosuria / L-xylulose reductase / L-xylulose reductase (NADPH) activity / xylulose metabolic process / glucuronate catabolic process to xylulose 5-phosphate / Formation of 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 / glucuronate catabolic process to xylulose 5-phosphate / Formation of 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 / microvillus / brush border / cytoplasmic microtubule / 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
DIHYDROGENPHOSPHATE ION / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-xylulose reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsEl-Kabbani, O. / Ishikura, S. / Darmanin, C. / Carbone, V. / Chung, R.P.-T. / Usami, N. / Hara, A.
Citation
Journal: Proteins / Year: 2004
Title: Crystal structure of human L-xylulose reductase holoenzyme: probing the role of Asn107 with site-directed mutagenesis
Authors: El-Kabbani, O. / Ishikura, S. / Darmanin, C. / Carbone, V. / Chung, R.P.-T. / Usami, N. / Hara, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and preliminary crystallographic analysis of human L-xylulose reductase
Authors: El-Kabbani, O. / Chung, R.P.-T. / Ishikura, S. / Usami, N. / Nakagawa, J. / Hara, A.
History
DepositionJun 20, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Apr 3, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)53,6418
Polymers51,8822
Non-polymers1,7596
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)107,28216
Polymers103,7644
Non-polymers3,51812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area20910 Å2
ΔGint-132 kcal/mol
Surface area29900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.111, 87.938, 72.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein L-XYLULOSE REDUCTASE /


Mass: 25941.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: kidney / Plasmid: pRset / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7Z4W1, L-xylulose reductase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION / Dihydrogen phosphate


Mass: 96.987 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O4P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.9 Å3/Da / Density % sol: 35.2 % / Description: ALL RESIDUES IN THE DIMER WERE DETERMINED
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, potassium phosphate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 295 K / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 %PEG80001reservoir
20.05 Mpotassium phosphate1reservoir
30.1 MMES1reservoirpH6.5
417 mg/mlprotein1drop
510 mMTris-HCl1droppH7.5
62 mM2-mercaptoethanol1drop
712.9 mMNADPH1drop

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 2001 / Details: MIRRORS
RadiationMonochromator: MAR MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
21.54181
ReflectionResolution: 1.96→20 Å / Num. all: 34738 / Num. obs: 34738 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.9
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3304 / % possible all: 96.61
Reflection
*PLUS
Num. measured all: 173378
Reflection shell
*PLUS
Highest resolution: 1.96 Å / % possible obs: 96.61 % / Num. unique obs: 3304 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
SHELXL-97refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MOUSE LUNG CARBONYL REDUCTASE

Resolution: 1.96→10 Å / Num. parameters: 15404 / Num. restraintsaints: 15309 / Isotropic thermal model: isptropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 1749 5 %RANDOM
Rwork0.1776 ---
all0.1786 34431 --
obs0.1783 32682 99.6 %-
Displacement parametersBiso mean: 22.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.075 Å / Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3911
Refinement stepCycle: LAST / Resolution: 1.96→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 108 172 3910
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0241
X-RAY DIFFRACTIONs_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.034
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.063
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.96→2.03 Å /
Num. reflection% reflection
obs3304 96.61 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rwork: 0.1786
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.73
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg11.53
X-RAY DIFFRACTIONs_plane_restr0.024
X-RAY DIFFRACTIONs_chiral_restr0.03

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