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- PDB-3sgz: High resolution crystal structure of rat long chain hydroxy acid ... -

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Basic information

Entry
Database: PDB / ID: 3sgz
TitleHigh resolution crystal structure of rat long chain hydroxy acid oxidase in complex with the inhibitor 4-carboxy-5-[(4-chiorophenyl)sulfanyl]-1, 2, 3-thiadiazole.
ComponentsHydroxyacid oxidase 2
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / FLAVOPROTEIN / HOMOLOGY / LONG CHAIN HYDROXY ACID OXIDASE / INHIBITOR / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


mandelate metabolic process / Peroxisomal lipid metabolism / Peroxisomal protein import / (S)-2-hydroxy-acid oxidase / (S)-2-hydroxy-acid oxidase activity / fatty acid alpha-oxidation / 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
FLAVIN MONONUCLEOTIDE / Chem-HO6 / 2-Hydroxyacid oxidase 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsChen, Z. / Vignaud, C. / Jaafar, A. / Gueritte, F. / Guenard, D. / Lederer, F. / Mathews, F.S.
Citation
Journal: Biochimie / Year: 2012
Title: High resolution crystal structure of rat long chain hydroxy acid oxidase in complex with the inhibitor 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1, 2, 3-thiadiazole. Implications for inhibitor ...Title: High resolution crystal structure of rat long chain hydroxy acid oxidase in complex with the inhibitor 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1, 2, 3-thiadiazole. Implications for inhibitor specificity and drug design.
Authors: Chen, Z.W. / Vignaud, C. / Jaafar, A. / Levy, B. / Gueritte, F. / Guenard, D. / Lederer, F. / Mathews, F.S.
#1: 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. / Diep Le, K.H. / Lederer, F. / Mathews, F.S.
History
DepositionJun 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Hydroxyacid oxidase 2
B: Hydroxyacid oxidase 2
C: Hydroxyacid oxidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,3039
Polymers117,1773
Non-polymers2,1266
Water19,8891104
1
A: Hydroxyacid oxidase 2
hetero molecules

A: Hydroxyacid oxidase 2
hetero molecules

A: Hydroxyacid oxidase 2
hetero molecules

A: Hydroxyacid oxidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,07112
Polymers156,2364
Non-polymers2,8358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area14860 Å2
ΔGint-64 kcal/mol
Surface area47660 Å2
MethodPISA
2
B: Hydroxyacid oxidase 2
hetero molecules

B: Hydroxyacid oxidase 2
hetero molecules

B: Hydroxyacid oxidase 2
hetero molecules

B: Hydroxyacid oxidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,07112
Polymers156,2364
Non-polymers2,8358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area15000 Å2
ΔGint-56 kcal/mol
Surface area46540 Å2
MethodPISA
3
C: Hydroxyacid oxidase 2
hetero molecules

C: Hydroxyacid oxidase 2
hetero molecules

C: Hydroxyacid oxidase 2
hetero molecules

C: Hydroxyacid oxidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,07112
Polymers156,2364
Non-polymers2,8358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area14810 Å2
ΔGint-60 kcal/mol
Surface area47450 Å2
MethodPISA
4
A: Hydroxyacid oxidase 2
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)318,14124
Polymers312,4728
Non-polymers5,66916
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area35080 Å2
ΔGint-164 kcal/mol
Surface area89950 Å2
MethodPISA
5
B: Hydroxyacid oxidase 2
hetero molecules

B: Hydroxyacid oxidase 2
hetero molecules

B: Hydroxyacid oxidase 2
hetero molecules

B: Hydroxyacid oxidase 2
hetero molecules

C: Hydroxyacid oxidase 2
hetero molecules

C: Hydroxyacid oxidase 2
hetero molecules

C: Hydroxyacid oxidase 2
hetero molecules

C: Hydroxyacid oxidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,14124
Polymers312,4728
Non-polymers5,66916
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_645y+1,-x-1,z1
Buried area34910 Å2
ΔGint-151 kcal/mol
Surface area88900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.450, 108.450, 491.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Hydroxyacid oxidase 2 / HAOX2 / (S)-2-hydroxy-acid oxidase / peroxisomal / Long chain alpha-hydroxy acid oxidase / Long- ...HAOX2 / (S)-2-hydroxy-acid oxidase / peroxisomal / Long chain alpha-hydroxy acid oxidase / Long-chain L-2-hydroxy acid oxidase


Mass: 39058.988 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hao2, Hao3, Haox2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07523, (S)-2-hydroxy-acid oxidase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-HO6 / 5-[(4-methylphenyl)sulfanyl]-1,2,3-thiadiazole-4-carboxylic acid / 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1, 2, 3-thiadiazole


Mass: 252.313 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H8N2O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1104 / 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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 295 K / pH: 6.5
Details: 2.8M NaCl and 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2006
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.35→40 Å / Num. obs: 311329 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 26.6
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.6 / % possible all: 94.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPfrom ccp4phasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TB3

1tb3


Resolution: 1.35→39.91 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 342133.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.203 15480 5 %RANDOM
Rwork0.185 ---
obs0.185 311329 98.1 %-
Displacement parametersBiso mean: 20.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.35→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7814 0 141 1104 9059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.23
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.35→1.43 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 2373 4.9 %
Rwork0.289 45811 -
obs--91.8 %

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