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

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Basic information

Entry
Database: PDB / ID: 8hdi
TitleBrucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: 1-53 truncation/K262T
Components7-alpha-hydroxysteroid dehydrogenase
KeywordsOXIDOREDUCTASE / SDR family / hydroxysteroid dehydrogenase
Function / homology
Function and homology information


7alpha-hydroxysteroid dehydrogenase / cholate 7-alpha-dehydrogenase (NAD+) activity / monocarboxylic acid metabolic process / lipid metabolic process / nucleotide binding
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 domain superfamily
Similarity search - Domain/homology
7-alpha-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesBrucella melitensis biotype 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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
DepositionNov 4, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,4184
Polymers103,4184
Non-polymers00
Water13,259736
1
A: 7-alpha-hydroxysteroid dehydrogenase
C: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)51,7092
Polymers51,7092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-28 kcal/mol
Surface area19550 Å2
MethodPISA
2
B: 7-alpha-hydroxysteroid dehydrogenase
D: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)51,7092
Polymers51,7092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-28 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.731, 99.731, 185.177
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
7-alpha-hydroxysteroid dehydrogenase


Mass: 25854.598 Da / Num. of mol.: 4 / Fragment: 1-53 truncation / Mutation: K262T
Source method: isolated from a genetically manipulated source
Details: Sequence reference for WP_014489477 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)
Gene: BMEI0406 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8YIN7, 7alpha-hydroxysteroid dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1M MIB, 10% PEG3350 / PH range: 4.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→43.18 Å / Num. obs: 73068 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 23.48 Å2 / CC1/2: 0.996 / Net I/σ(I): 15.5
Reflection shellResolution: 1.99→2.07 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 6.6 / Num. unique obs: 73517 / CC1/2: 0.972 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→42.06 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 3566 4.88 %
Rwork0.1726 --
obs0.1745 73068 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→42.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6924 0 0 736 7660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077058
X-RAY DIFFRACTIONf_angle_d0.9039557
X-RAY DIFFRACTIONf_dihedral_angle_d5.58999
X-RAY DIFFRACTIONf_chiral_restr0.061108
X-RAY DIFFRACTIONf_plane_restr0.0091260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.23441320.1712606X-RAY DIFFRACTION96
2.02-2.050.20771400.16252723X-RAY DIFFRACTION100
2.05-2.080.23141320.16862829X-RAY DIFFRACTION100
2.08-2.110.19361280.15912724X-RAY DIFFRACTION100
2.11-2.150.22771350.17582773X-RAY DIFFRACTION100
2.15-2.180.21711510.1722749X-RAY DIFFRACTION100
2.18-2.220.21361480.17762743X-RAY DIFFRACTION100
2.22-2.270.28591490.20982765X-RAY DIFFRACTION100
2.27-2.310.24491640.19542749X-RAY DIFFRACTION100
2.31-2.360.20781170.17622773X-RAY DIFFRACTION100
2.36-2.420.2091330.17272773X-RAY DIFFRACTION100
2.42-2.480.21921490.17272775X-RAY DIFFRACTION100
2.48-2.550.21561430.17822753X-RAY DIFFRACTION100
2.55-2.620.21851570.17622785X-RAY DIFFRACTION100
2.62-2.710.19811500.18042760X-RAY DIFFRACTION100
2.71-2.80.24571250.18462783X-RAY DIFFRACTION100
2.8-2.910.22371230.17682810X-RAY DIFFRACTION100
2.91-3.050.23881460.17972792X-RAY DIFFRACTION100
3.05-3.210.21751980.18282738X-RAY DIFFRACTION100
3.21-3.410.25461340.17862793X-RAY DIFFRACTION100
3.41-3.670.18671680.16542810X-RAY DIFFRACTION100
3.67-4.040.22421010.16292859X-RAY DIFFRACTION100
4.04-4.620.16081580.14262810X-RAY DIFFRACTION99
4.63-5.820.17241190.16562911X-RAY DIFFRACTION100
5.83-42.060.21161660.18272916X-RAY DIFFRACTION97

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