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- PDB-1tb3: Crystal Structure Analysis of Recombinant Rat Kidney Long-chain H... -

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Basic information

Entry
Database: PDB / ID: 1tb3
TitleCrystal Structure Analysis of Recombinant Rat Kidney Long-chain Hydroxy Acid Oxidase
ComponentsHydroxyacid oxidase 3
KeywordsOXIDOREDUCTASE / long chain alpha-hydroxy acid oxidase / flavoprotein / oxidase
Function / homology
Function and homology information


mandelate metabolic process / Peroxisomal lipid metabolism / Peroxisomal protein import / (S)-2-hydroxy-acid oxidase / fatty acid alpha-oxidation / (S)-2-hydroxy-acid oxidase activity / fatty acid oxidation / peroxisomal matrix / peroxisome / FMN binding / identical protein binding
Similarity search - Function
Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FLAVIN MONONUCLEOTIDE / 2-Hydroxyacid oxidase 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCunane, L.M. / Barton, J.D. / Chen, Z.W. / Le, K.H.D. / Amar, D. / Lederer, F. / Mathews, F.S.
Citation
Journal: Biochemistry / Year: 2005
Title: Crystal Structure Analysis of Recombinant Rat Kidney Long Chain Hydroxy Acid Oxidase.
Authors: Cunane, L.M. / Barton, J.D. / Chen, Z.W. / Le, K.H.D. / Amar, D. / Lederer, F. / Mathews, F.S.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Refined structure of spinach glycolate oxidase at 2 A resolution.
Authors: Lindqvist, Y.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Molecular structure of flavocytochrome b2 at 2.4 A resolution.
Authors: Xia, Z. / Mathews, F.S.
History
DepositionMay 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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: Hydroxyacid oxidase 3
B: Hydroxyacid oxidase 3
C: Hydroxyacid oxidase 3
D: Hydroxyacid oxidase 3
E: Hydroxyacid oxidase 3
F: Hydroxyacid oxidase 3
G: Hydroxyacid oxidase 3
H: Hydroxyacid oxidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,08324
Polymers312,9528
Non-polymers4,13116
Water16,214900
1
A: Hydroxyacid oxidase 3
B: Hydroxyacid oxidase 3
C: Hydroxyacid oxidase 3
D: Hydroxyacid oxidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,54212
Polymers156,4764
Non-polymers2,0668
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14440 Å2
ΔGint-57 kcal/mol
Surface area45580 Å2
MethodPISA
2
E: Hydroxyacid oxidase 3
F: Hydroxyacid oxidase 3
G: Hydroxyacid oxidase 3
H: Hydroxyacid oxidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,54212
Polymers156,4764
Non-polymers2,0668
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint-56 kcal/mol
Surface area45410 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31670 Å2
ΔGint-128 kcal/mol
Surface area88180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.839, 151.100, 222.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Hydroxyacid oxidase 3 / HAOX3 / (S)-2-hydroxy-acid oxidase / peroxisomal / Long chain alpha-hydroxy acid oxidase / Long- ...HAOX3 / (S)-2-hydroxy-acid oxidase / peroxisomal / Long chain alpha-hydroxy acid oxidase / Long-chain L-2-hydroxy acid oxidase


Mass: 39119.000 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: HAO3, HAOX3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07523, (S)-2-hydroxy-acid oxidase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 900 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium acetate, sodium citrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: SBC / Detector: CCD / Date: Apr 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 171648 / Num. obs: 159633 / % possible obs: 93 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.4 / Num. unique all: 6770 / % possible all: 79.4

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GOX

1gox


Resolution: 2.3→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 7147 -RANDOM
Rwork0.239 ---
all-171664 --
obs-142711 83.1 %-
Displacement parametersBiso mean: 39.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20425 0 248 932 21605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
2.3-2.440.37478810.3172X-RAY DIFFRACTION170616
2.44-2.630.35079890.2952X-RAY DIFFRACTION194386
2.63-2.90.312711170.275X-RAY DIFFRACTION220076
2.9-3.320.2913530.2563X-RAY DIFFRACTION244226
3.32-4.180.259413990.2291X-RAY DIFFRACTION258486
4.18-38.910.211214080.1963X-RAY DIFFRACTION267886

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