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- PDB-6pzn: Putative SDR from Acinetobacter baumannii Crystal Form 2 -

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Basic information

Entry
Database: PDB / ID: 6pzn
TitlePutative SDR from Acinetobacter baumannii Crystal Form 2
Components3-ketoacyl-ACP reductase
KeywordsOXIDOREDUCTASE / Short-chain dehydrogenase/reductase / SDR / Rossmann fold / apo / FabG
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 3-ketoacyl-ACP reductase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCross, E.M. / Aragao, D. / Forwood, J.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structural characterization of a short-chain dehydrogenase/reductase from multi-drug resistant Acinetobacter baumannii.
Authors: Cross, E.M. / Aragao, D. / Smith, K.M. / Shaw, K.I. / Nanson, J.D. / Raidal, S.R. / Forwood, J.K.
History
DepositionAug 1, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionAug 14, 2019ID: 6OV5
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 29, 2023Group: Database references / Category: citation_author / database_2
Item: _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-ketoacyl-ACP reductase
B: 3-ketoacyl-ACP reductase
C: 3-ketoacyl-ACP reductase
D: 3-ketoacyl-ACP reductase


Theoretical massNumber of molelcules
Total (without water)113,9134
Polymers113,9134
Non-polymers00
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12300 Å2
ΔGint-81 kcal/mol
Surface area35330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.620, 89.960, 130.529
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
3-ketoacyl-ACP reductase / Short Chain Dehydrogenase Reductase


Mass: 28478.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: A7M90_05510, CBE85_12250 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S2FVD8, Oxidoreductases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES, pH 7.5, 0.8 M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2→45.24 Å / Num. obs: 70331 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.93 Å2 / CC1/2: 0.843 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.06 / Rrim(I) all: 0.116 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4491 / CC1/2: 0.772 / Rpim(I) all: 0.207 / Rrim(I) all: 0.405

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHASERphasing
Aimlessdata scaling
iMOSFLMdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3U5T

3u5t


Resolution: 2→45.24 Å / SU ML: 0.2137 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.921
RfactorNum. reflection% reflection
Rfree0.2229 3658 5.21 %
Rwork0.1858 --
obs0.1877 70232 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.38 Å2
Refinement stepCycle: LAST / Resolution: 2→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7222 0 0 456 7678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00697346
X-RAY DIFFRACTIONf_angle_d0.78119983
X-RAY DIFFRACTIONf_chiral_restr0.05481164
X-RAY DIFFRACTIONf_plane_restr0.00611321
X-RAY DIFFRACTIONf_dihedral_angle_d10.53944393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.251470.20332533X-RAY DIFFRACTION100
2.03-2.050.27291510.20072511X-RAY DIFFRACTION100
2.05-2.080.26221450.20292541X-RAY DIFFRACTION99.96
2.08-2.110.25231530.20472488X-RAY DIFFRACTION99.77
2.11-2.150.27421360.20212547X-RAY DIFFRACTION99.85
2.15-2.180.27081670.19532498X-RAY DIFFRACTION99.93
2.18-2.220.24271410.19842503X-RAY DIFFRACTION99.89
2.22-2.260.27991350.19732548X-RAY DIFFRACTION99.52
2.26-2.30.27561530.19772539X-RAY DIFFRACTION99.93
2.3-2.350.25041270.19672525X-RAY DIFFRACTION99.7
2.35-2.40.25631510.1982527X-RAY DIFFRACTION99.48
2.4-2.460.25261570.19692533X-RAY DIFFRACTION100
2.46-2.520.24921330.19532557X-RAY DIFFRACTION100
2.52-2.590.27431110.20782570X-RAY DIFFRACTION99.93
2.59-2.660.26821140.20852588X-RAY DIFFRACTION99.96
2.66-2.750.23831120.20542579X-RAY DIFFRACTION100
2.75-2.850.25151330.21032559X-RAY DIFFRACTION99.96
2.85-2.960.25011240.21222571X-RAY DIFFRACTION99.93
2.96-3.10.23861340.21212574X-RAY DIFFRACTION99.89
3.1-3.260.24031300.21942563X-RAY DIFFRACTION99.7
3.26-3.460.24511340.18752576X-RAY DIFFRACTION99.38
3.46-3.730.17711380.16912587X-RAY DIFFRACTION100
3.73-4.110.18751310.15582618X-RAY DIFFRACTION100
4.11-4.70.18081700.14052579X-RAY DIFFRACTION100
4.7-5.920.19021560.16472627X-RAY DIFFRACTION99.54
5.92-45.240.15681750.1582733X-RAY DIFFRACTION99.49

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