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

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Basic information

Entry
Database: PDB / ID: 8hsa
TitleBrucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: 1-53 truncation/M196I/I258M/K262T-NAD+
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 7-alpha-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesBrucella melitensis biotype 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 18, 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
G: 7-alpha-hydroxysteroid dehydrogenase
A: 7-alpha-hydroxysteroid dehydrogenase
B: 7-alpha-hydroxysteroid dehydrogenase
C: 7-alpha-hydroxysteroid dehydrogenase
D: 7-alpha-hydroxysteroid dehydrogenase
E: 7-alpha-hydroxysteroid dehydrogenase
F: 7-alpha-hydroxysteroid dehydrogenase
H: 7-alpha-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,38016
Polymers203,0738
Non-polymers5,3078
Water00
1
G: 7-alpha-hydroxysteroid dehydrogenase
B: 7-alpha-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0954
Polymers50,7682
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-40 kcal/mol
Surface area19730 Å2
MethodPISA
2
A: 7-alpha-hydroxysteroid dehydrogenase
C: 7-alpha-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0954
Polymers50,7682
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-41 kcal/mol
Surface area19660 Å2
MethodPISA
3
D: 7-alpha-hydroxysteroid dehydrogenase
F: 7-alpha-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0954
Polymers50,7682
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-43 kcal/mol
Surface area19560 Å2
MethodPISA
4
E: 7-alpha-hydroxysteroid dehydrogenase
hetero molecules

H: 7-alpha-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0954
Polymers50,7682
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4810 Å2
ΔGint-36 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.931, 108.647, 130.883
Angle α, β, γ (deg.)90.00, 96.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
7-alpha-hydroxysteroid dehydrogenase / Short-chain dehydrogenase/reductase SDR


Mass: 25384.078 Da / Num. of mol.: 8 / Mutation: M196I/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
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M Sodium formate, 20% PEG ester 5000

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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: 3→23.84 Å / Num. obs: 68427 / % possible obs: 96.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 39.3 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.155 / Net I/σ(I): 7.5
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 35933 / CC1/2: 0.885

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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: 3→23.84 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3149 3758 5.49 %
Rwork0.225 --
obs0.23 68420 92.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→23.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14071 0 352 0 14423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114677
X-RAY DIFFRACTIONf_angle_d1.26419940
X-RAY DIFFRACTIONf_dihedral_angle_d10.1462065
X-RAY DIFFRACTIONf_chiral_restr0.0642318
X-RAY DIFFRACTIONf_plane_restr0.0112571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.040.37551340.332386X-RAY DIFFRACTION90
3.04-3.080.46371420.30172462X-RAY DIFFRACTION94
3.08-3.120.36981400.29442458X-RAY DIFFRACTION94
3.12-3.160.37211440.28942411X-RAY DIFFRACTION94
3.16-3.210.41321450.30322506X-RAY DIFFRACTION94
3.21-3.260.43291420.28562362X-RAY DIFFRACTION94
3.26-3.310.36321380.28972405X-RAY DIFFRACTION93
3.31-3.370.38231470.2972494X-RAY DIFFRACTION93
3.37-3.430.38591380.27812379X-RAY DIFFRACTION93
3.43-3.50.42161390.25242411X-RAY DIFFRACTION93
3.5-3.570.37751460.24982439X-RAY DIFFRACTION93
3.57-3.650.35241430.24942391X-RAY DIFFRACTION93
3.65-3.730.34461420.23812420X-RAY DIFFRACTION93
3.73-3.820.33421390.24922391X-RAY DIFFRACTION93
3.83-3.930.31211390.23472419X-RAY DIFFRACTION93
3.93-4.040.31021470.22142426X-RAY DIFFRACTION93
4.04-4.170.27521390.20052369X-RAY DIFFRACTION92
4.17-4.320.24381290.19932421X-RAY DIFFRACTION92
4.32-4.490.27351430.18432376X-RAY DIFFRACTION92
4.49-4.70.27871370.18322388X-RAY DIFFRACTION92
4.7-4.940.27111400.17682397X-RAY DIFFRACTION91
4.94-5.250.27861350.18722379X-RAY DIFFRACTION92
5.25-5.650.27031390.19712335X-RAY DIFFRACTION90
5.65-6.210.27921320.20662353X-RAY DIFFRACTION91
6.21-7.090.30711340.19132350X-RAY DIFFRACTION91
7.09-8.850.21151390.15652332X-RAY DIFFRACTION90
8.85-23.840.20261260.15152202X-RAY DIFFRACTION84

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