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- PDB-8hs9: Brucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant:I... -

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Basic information

Entry
Database: PDB / ID: 8hs9
TitleBrucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant:I258M/K262T
Components7-alpha-hydroxysteroid dehydrogenase
KeywordsOXIDOREDUCTASE / SDR family / hydroxysteroid dehydrogenase
Function / homology7alpha-hydroxysteroid dehydrogenase / cholate 7-alpha-dehydrogenase activity / 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 domain superfamily / 7-alpha-hydroxysteroid dehydrogenase
Function and homology information
Biological speciesBrucella melitensis biotype 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsLiu, Z.Y. / Zhang, R.Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31970045 China
National Science Foundation (NSF, China)32271487 China
CitationJournal: To Be Published
Title: Structure of 7-alpha-hydroxysteroid dehydrogenase
Authors: Liu, Z.Y. / Zhang, R.Z.
History
DepositionDec 17, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 7-alpha-hydroxysteroid dehydrogenase
A: 7-alpha-hydroxysteroid dehydrogenase
B: 7-alpha-hydroxysteroid dehydrogenase
C: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)102,9664
Polymers102,9664
Non-polymers00
Water0
1
E: 7-alpha-hydroxysteroid dehydrogenase
B: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)51,4832
Polymers51,4832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-31 kcal/mol
Surface area19800 Å2
MethodPISA
2
E: 7-alpha-hydroxysteroid dehydrogenase
C: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)51,4832
Polymers51,4832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-26 kcal/mol
Surface area19470 Å2
MethodPISA
3
A: 7-alpha-hydroxysteroid dehydrogenase
C: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)51,4832
Polymers51,4832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-32 kcal/mol
Surface area19560 Å2
MethodPISA
4
A: 7-alpha-hydroxysteroid dehydrogenase
B: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)51,4832
Polymers51,4832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-26 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.768, 54.813, 76.505
Angle α, β, γ (deg.)82.94, 70.65, 81.29
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
7-alpha-hydroxysteroid dehydrogenase


Mass: 25741.438 Da / Num. of mol.: 4 / Mutation: I258M/K262T
Source method: isolated from a genetically manipulated source
Details: Author stated: in our study, wild-type 7alpha-hydroxysteroid dehydrogenase (protein_id="QEX87556.1") from Brucella melis strain RM57(RM57CP044342.1) was cloned into E. coli. Sequence ...Details: Author stated: in our study, wild-type 7alpha-hydroxysteroid dehydrogenase (protein_id="QEX87556.1") from Brucella melis strain RM57(RM57CP044342.1) was cloned into E. coli. Sequence reference for strain RM57 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id Q8YIN7.
Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria)
Strain: RM57 / Gene: BMEI0406 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8YIN7, 7alpha-hydroxysteroid dehydrogenase

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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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M BIS-TRIS, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.25→23.342 Å / Num. obs: 12956 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.182 / Rrim(I) all: 0.202 / Net I/σ(I): 6.2
Reflection shellResolution: 3.25→3.37 Å / Rmerge(I) obs: 0.462 / Num. unique obs: 12915 / CC1/2: 0.913

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→23.342 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.93 / Phase error: 32.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2853 692 5.36 %
Rwork0.2404 --
obs0.2429 12915 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→23.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6754 0 0 0 6754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037019
X-RAY DIFFRACTIONf_angle_d0.6089491
X-RAY DIFFRACTIONf_dihedral_angle_d6.1964183
X-RAY DIFFRACTIONf_chiral_restr0.0461091
X-RAY DIFFRACTIONf_plane_restr0.0061250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2501-3.50030.33191500.26522422X-RAY DIFFRACTION100
3.5003-3.85120.31191440.25812451X-RAY DIFFRACTION100
3.8512-4.40520.3141130.2422453X-RAY DIFFRACTION99
4.4052-5.53780.26371230.23342495X-RAY DIFFRACTION100
5.5378-23.3420.24981620.22122402X-RAY DIFFRACTION99

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