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- PDB-1gz6: (3R)-HYDROXYACYL-COA DEHYDROGENASE FRAGMENT OF RAT PEROXISOMAL MU... -

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Basic information

Entry
Database: PDB / ID: 1gz6
Title(3R)-HYDROXYACYL-COA DEHYDROGENASE FRAGMENT OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE 2
ComponentsESTRADIOL 17 BETA-DEHYDROGENASE 4
KeywordsDEHYDROGENASE / 17BETA-HSD4 / MFE-2 / BETA-OXIDATION / PEROXISOME / SDR / STEROID BIOSYNTHESIS / OXIDOREDUCTASE / NADP / MULTIGENE FAMIL
Function / homology
Function and homology information


Beta-oxidation of pristanoyl-CoA / alpha-linolenic acid (ALA) metabolism / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase / 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity / very long-chain fatty-acyl-CoA metabolic process / medium-chain fatty-acyl-CoA metabolic process / : / (3R)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / Beta-oxidation of very long chain fatty acids ...Beta-oxidation of pristanoyl-CoA / alpha-linolenic acid (ALA) metabolism / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase / 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity / very long-chain fatty-acyl-CoA metabolic process / medium-chain fatty-acyl-CoA metabolic process / : / (3R)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / Beta-oxidation of very long chain fatty acids / enoyl-CoA hydratase 2 / 3-hydroxyacyl-CoA dehydratase activity / Peroxisomal protein import / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / very long-chain fatty acid metabolic process / 3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / testosterone dehydrogenase [NAD(P)+] activity / Sertoli cell development / enoyl-CoA hydratase activity / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / estrogen metabolic process / response to steroid hormone / fatty acid beta-oxidation / : / androgen metabolic process / cholesterol metabolic process / isomerase activity / : / peroxisome / response to xenobiotic stimulus / protein homodimerization activity / identical protein binding
Similarity search - Function
Helix Hairpins - #4290 / : / MFE-2 hydratase 2 N-terminal domain / : / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily ...Helix Hairpins - #4290 / : / MFE-2 hydratase 2 N-terminal domain / : / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain superfamily / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase SDR / Helix Hairpins / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Peroxisomal multifunctional enzyme type 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.38 Å
AuthorsHaapalainen, A.M. / Hiltunen, J.K. / Glumoff, T.
CitationJournal: Structure / Year: 2003
Title: Binary Structure of the Two-Domain (3R)-Hydroxyacyl-Coa Dehydrogenase from Rat Peroxisomal Multifunctional Enzyme Type 2 at 2.38 A Resolution
Authors: Haapalainen, A.M. / Koski, M.K. / Qin, Y.M. / Hiltunen, J.K. / Glumoff, T.
History
DepositionMay 16, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESTRADIOL 17 BETA-DEHYDROGENASE 4
B: ESTRADIOL 17 BETA-DEHYDROGENASE 4
C: ESTRADIOL 17 BETA-DEHYDROGENASE 4
D: ESTRADIOL 17 BETA-DEHYDROGENASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,43213
Polymers139,2904
Non-polymers3,1429
Water14,718817
1
A: ESTRADIOL 17 BETA-DEHYDROGENASE 4
B: ESTRADIOL 17 BETA-DEHYDROGENASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2647
Polymers69,6452
Non-polymers1,6195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: ESTRADIOL 17 BETA-DEHYDROGENASE 4
D: ESTRADIOL 17 BETA-DEHYDROGENASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1686
Polymers69,6452
Non-polymers1,5234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)89.466, 82.748, 95.745
Angle α, β, γ (deg.)90.00, 94.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9884, -0.0005, 0.1522), (-0.0006, -1, 0.0003), (0.1522, -0.0004, -0.9884)
Vector: 180, 359.849, 85.632)

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Components

#1: Protein
ESTRADIOL 17 BETA-DEHYDROGENASE 4 / 17-BETA-HSD 4 / 17-BETA-HYDROXYSTEROID DEHYDROGENASE / HSD IV17-BETA-HSD 4


Mass: 34822.527 Da / Num. of mol.: 4
Fragment: (3R)-HYDROXYACYL-COA DEHYDROGENASE FRAGMENT, RESIDUES 1-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: LIVER / Plasmid: PET3D/DHDELTASCP-2LDELTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P97852, 17beta-estradiol 17-dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51 %
Crystal growpH: 5.5
Details: 21 % PEG 6000, 0.2 M LITHIUM SULFATE 0.1 M NA-CACODYLATE, PH 5.5, 10 MM NAD+, 0.23 MM TRITON X-100
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
121 %(w/v)PEG60001reservoir
20.2 M1reservoirLi2SO4
30.1 Msodium cacodylate1reservoirpH5.5
43.9 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979578,0.979269,0.972433
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2000 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9795781
20.9792691
30.9724331
ReflectionResolution: 2.38→20 Å / Num. obs: 55717 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 12.9
Reflection shellResolution: 2.38→2.46 Å / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 6.6 / % possible all: 98.4
Reflection
*PLUS
Lowest resolution: 24 Å
Reflection shell
*PLUS
% possible obs: 98.4 % / Num. unique obs: 5466

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.38→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2809 5.1 %RANDOM
Rwork0.197 ---
obs0.197 55603 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.1235 Å2 / ksol: 0.352456 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.55 Å20 Å2-2.02 Å2
2---11.36 Å20 Å2
3---2.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.38→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8943 0 201 817 9961
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
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
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 2.38→2.52 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 457 5.1 %
Rwork0.194 8510 -
obs--96.2 %
Xplor fileSerial no: 1 / Param file: NAI_XPLOR_PAR.TXT / Topol file: NAI_XPLOR_TOP.TXT
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection all: 55603 / Num. reflection obs: 52794
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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