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

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Basic information

Entry
Database: PDB / ID: 8hdn
TitleBrucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: 1-53 truncation-I258M/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: 1.7 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 5, 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
C: 7-alpha-hydroxysteroid dehydrogenase
D: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)103,4914
Polymers103,4914
Non-polymers00
Water14,646813
1
A: 7-alpha-hydroxysteroid dehydrogenase
B: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)51,7452
Polymers51,7452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-31 kcal/mol
Surface area20090 Å2
MethodPISA
2
A: 7-alpha-hydroxysteroid dehydrogenase
C: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)51,7452
Polymers51,7452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-26 kcal/mol
Surface area20380 Å2
MethodPISA
3
B: 7-alpha-hydroxysteroid dehydrogenase
D: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)51,7452
Polymers51,7452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-26 kcal/mol
Surface area20350 Å2
MethodPISA
4
C: 7-alpha-hydroxysteroid dehydrogenase
D: 7-alpha-hydroxysteroid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)51,7452
Polymers51,7452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-31 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.402, 100.402, 92.221
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
7-alpha-hydroxysteroid dehydrogenase


Mass: 25872.635 Da / Num. of mol.: 4 / Fragment: 1-53 truncation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria)
Gene: BMEI0406 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8YIN7, 7alpha-hydroxysteroid dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 813 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M MIB, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / 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: 1.7→44.13 Å / Num. obs: 113642 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 12.68 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.044 / Rrim(I) all: 0.139 / Net I/σ(I): 10.9
Reflection shellResolution: 1.7→1.763 Å / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 10.9 / Num. unique obs: 11259 / CC1/2: 0.865 / Rpim(I) all: 0.334 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIX(1.20.1_4487: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GAF, 1FMC

3gaf

1fmc


Resolution: 1.7→33.96 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 981 -RANDOM
Rwork0.1777 ---
obs0.178 113623 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7006 0 0 813 7819
Refine LS restraintsType: f_bond_d / Dev ideal: 0.006 / Number: 7141
LS refinement shellResolution: 1.7→1.79 Å
RfactorNum. reflection% reflection
Rfree0.2063 125 -
Rwork0.1816 16049 -
obs--99 %

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