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- PDB-8eh2: Short-chain dehydrogenase/reductase (SDR) from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 8eh2
TitleShort-chain dehydrogenase/reductase (SDR) from Acinetobacter baumannii
ComponentsSDR family oxidoreductase
KeywordsOXIDOREDUCTASE / Short-chain / SDR
Function / homology3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / SDR family oxidoreductase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShaw, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Short-chain dehydrogenase/reductase (SDR) from Acinetobacter baumannii
Authors: Forwood, J.K.
History
DepositionSep 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SDR family oxidoreductase
B: SDR family oxidoreductase


Theoretical massNumber of molelcules
Total (without water)55,6552
Polymers55,6552
Non-polymers00
Water3,621201
1
A: SDR family oxidoreductase
B: SDR family oxidoreductase

A: SDR family oxidoreductase
B: SDR family oxidoreductase


Theoretical massNumber of molelcules
Total (without water)111,3104
Polymers111,3104
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area17910 Å2
ΔGint-139 kcal/mol
Surface area33620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.431, 109.460, 136.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-372-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 259 / Label seq-ID: 1 - 259

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and (resid 1 through 185 or (resid 186...AA
22(chain 'B' and (resid 1 through 51 or (resid 52...BB

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Components

#1: Protein SDR family oxidoreductase


Mass: 27827.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: F4T85_19375, FJU42_12090, HBK86_07635 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3FP68
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M lithium chloride, 0.1M Tris pH 8.0, 20% (v/v) polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: 80 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→29.4 Å / Num. obs: 20194 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 0.986 / Net I/σ(I): 6.9
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 2085 / CC1/2: 0.819

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D1Y

2d1y


Resolution: 2.4→29.4 Å / SU ML: 0.2284 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5445 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2257 1117 5.54 %
Rwork0.1899 19033 -
obs0.1919 20150 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.76 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3845 0 0 201 4046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223910
X-RAY DIFFRACTIONf_angle_d0.49345327
X-RAY DIFFRACTIONf_chiral_restr0.042634
X-RAY DIFFRACTIONf_plane_restr0.0028688
X-RAY DIFFRACTIONf_dihedral_angle_d2.33832309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.28081340.22582325X-RAY DIFFRACTION99.47
2.51-2.640.30851310.21772350X-RAY DIFFRACTION100
2.64-2.810.27191200.222401X-RAY DIFFRACTION99.76
2.81-3.020.23451460.21462325X-RAY DIFFRACTION99.92
3.02-3.330.21981510.1932344X-RAY DIFFRACTION99.92
3.33-3.810.22291330.17772407X-RAY DIFFRACTION99.84
3.81-4.790.18961380.15722404X-RAY DIFFRACTION99.84
4.79-29.40.20631640.18462477X-RAY DIFFRACTION99.62

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