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

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Basic information

Entry
Database: PDB / ID: 8hde
TitleBrucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: 1-53 truncation/I258M
Components7-alpha-hydroxysteroid dehydrogenase
KeywordsOXIDOREDUCTASE / SDR family / hydroxysteroid dehydrogenase
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6634
Polymers51,5392
Non-polymers1242
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.260, 98.260, 92.456
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21A-576-

HOH

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Components

#1: Protein 7-alpha-hydroxysteroid dehydrogenase


Mass: 25769.514 Da / Num. of mol.: 2 / Fragment: 1-53 truncation / Mutation: I258M
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Brucella melitensis is not available in UniProt at the time of biocuration. Current sequence reference is from GenBank id QEX87556.1.
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: RM57 / Gene: hdhA / Production host: Escherichia coli (E. coli) / References: 7alpha-hydroxysteroid dehydrogenase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.5 Å3/Da / Density % sol: 50.8 % / Description: orthorhombic
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1M MIB buffer, 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: 1 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Dec 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→23.6 Å / Num. obs: 27394 / % possible obs: 99.6 % / Redundancy: 10 % / CC1/2: 0.996 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.05 / Rrim(I) all: 0.158 / Net I/σ(I): 13
Reflection shellResolution: 2.7→2.79 Å / Num. unique obs: 14529 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GAF,1FMC

3gaf

1fmc


Resolution: 2.7→23.6 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 2722 9.94 %RANDOM
Rwork0.1753 ---
obs0.1842 27387 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→23.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3489 0 8 149 3646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.968
X-RAY DIFFRACTIONf_dihedral_angle_d6.663503
X-RAY DIFFRACTIONf_chiral_restr0.057550
X-RAY DIFFRACTIONf_plane_restr0.008634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.31221380.26491231X-RAY DIFFRACTION94
2.75-2.80.3251340.25441318X-RAY DIFFRACTION100
2.8-2.860.34961440.2291280X-RAY DIFFRACTION100
2.86-2.920.34341480.21891298X-RAY DIFFRACTION100
2.92-2.990.35671480.2281327X-RAY DIFFRACTION100
2.99-3.060.34881460.23831295X-RAY DIFFRACTION100
3.06-3.140.34331480.20951284X-RAY DIFFRACTION100
3.14-3.230.25071480.21181273X-RAY DIFFRACTION100
3.24-3.340.30181400.20681319X-RAY DIFFRACTION100
3.34-3.460.311500.1751311X-RAY DIFFRACTION100
3.46-3.60.27461410.17621287X-RAY DIFFRACTION100
3.6-3.760.27291440.15441311X-RAY DIFFRACTION100
3.76-3.960.28281400.16031328X-RAY DIFFRACTION100
3.96-4.20.22841420.1421287X-RAY DIFFRACTION100
4.2-4.530.18961410.12921314X-RAY DIFFRACTION100
4.53-4.980.22721460.13431297X-RAY DIFFRACTION100
4.98-5.690.23781500.14841292X-RAY DIFFRACTION100
5.69-7.130.21891380.16371308X-RAY DIFFRACTION100
7.14-23.60.18531360.14161305X-RAY DIFFRACTION99

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