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- PDB-8hax: Brucella melitensis 7alpha-Hydroxysteroid Dehydrogenase mutant-I2... -

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Basic information

Entry
Database: PDB / ID: 8hax
TitleBrucella melitensis 7alpha-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 / 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 7alpha-hydroxysteroid dehydrogenase
Authors: Liu, Z.Y. / Zhang, R.Z.
History
DepositionOct 27, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 1, 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
C: 7-alpha-hydroxysteroid dehydrogenase
D: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)127,5144
Polymers127,5144
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-114 kcal/mol
Surface area34070 Å2
MethodPISA
2
A: 7-alpha-hydroxysteroid dehydrogenase
C: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)63,7572
Polymers63,7572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-31 kcal/mol
Surface area19900 Å2
MethodPISA
3
A: 7-alpha-hydroxysteroid dehydrogenase
D: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)63,7572
Polymers63,7572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-27 kcal/mol
Surface area20170 Å2
MethodPISA
4
B: 7-alpha-hydroxysteroid dehydrogenase
D: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)63,7572
Polymers63,7572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-31 kcal/mol
Surface area20220 Å2
MethodPISA
5
B: 7-alpha-hydroxysteroid dehydrogenase
C: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)63,7572
Polymers63,7572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-26 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.768, 54.813, 76.505
Angle α, β, γ (deg.)82.940, 70.650, 81.290
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 31878.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria)
Gene: BMEI0406, BAWG_2387
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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: 1.67 Å3/Da / Density % sol: 26.55 % / Description: Rhombohedral crystal
Crystal growTemperature: 289.15 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: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 0.9875 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 3.25→23.342 Å / Num. obs: 12915 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 59.84 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.087 / Rrim(I) all: 0.202 / Net I/σ(I): 6.2
Reflection shellResolution: 3.25→3.36 Å / Num. unique obs: 12888 / CC1/2: 0.989

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
HKL-30007.21data scaling
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHENIX1.18.2-3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FMC, 3GAF

1fmc

3gaf


Resolution: 3.25→23.342 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 32.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2853 692 5.36 %
Rwork0.2395 --
obs0.2429 12915 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.35 Å2 / Biso mean: 59.8383 Å2 / Biso min: 15.09 Å2
Refinement stepCycle: final / Resolution: 3.25→23.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6908 0 0 0 6908
Num. residues----961

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