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- PDB-8hs4: Brucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: ... -

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Basic information

Entry
Database: PDB / ID: 8hs4
TitleBrucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: 1-53 truncation/K262T-NAD+
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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 7-alpha-hydroxysteroid dehydrogenase
Function and homology information
Biological speciesBrucella melitensis biotype 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

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Assembly

Deposited unit
A: 7-alpha-hydroxysteroid dehydrogenase
B: 7-alpha-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3174
Polymers50,9902
Non-polymers1,3272
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-36 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.204, 98.204, 93.144
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 7-alpha-hydroxysteroid dehydrogenase


Mass: 25495.154 Da / Num. of mol.: 2 / Mutation: 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
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
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: 0.9875 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: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2→40.88 Å / Num. obs: 72757 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.118 / Net I/σ(I): 15.5
Reflection shellResolution: 2→2.073 Å / Num. unique obs: 72757 / CC1/2: 0.973

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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: 2→40.85 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 2005 5.7 %RANDOM
Rwork0.176 ---
obs0.1777 35163 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 0 145 3639
Refine LS restraintsType: f_plane_restr / Dev ideal: 0.01 / Number: 626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2291360.18472297X-RAY DIFFRACTION98
2.05-2.110.26171450.16982334X-RAY DIFFRACTION99
2.11-2.170.19111410.17972313X-RAY DIFFRACTION99
2.17-2.240.18581460.16042336X-RAY DIFFRACTION99
2.24-2.320.19681380.16882353X-RAY DIFFRACTION99
2.32-2.410.21651420.16452344X-RAY DIFFRACTION99
2.41-2.520.21721430.182370X-RAY DIFFRACTION99
2.52-2.650.21651430.18032388X-RAY DIFFRACTION100
2.65-2.820.23881440.192347X-RAY DIFFRACTION100
2.82-3.040.22091450.18222364X-RAY DIFFRACTION100
3.04-3.340.22331410.18822389X-RAY DIFFRACTION100
3.34-3.830.19341420.16592415X-RAY DIFFRACTION100
3.83-4.820.18711460.16182418X-RAY DIFFRACTION99
4.83-40.850.18991530.18932490X-RAY DIFFRACTION99

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