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- PDB-3e9q: Crystal Structure of the Short Chain Dehydrogenase from Shigella ... -

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Basic information

Entry
Database: PDB / ID: 3e9q
TitleCrystal Structure of the Short Chain Dehydrogenase from Shigella flexneri
ComponentsShort-chain dehydrogenase
KeywordsOXIDOREDUCTASE / alpha-beta-alpha sandwich / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Oxidoreductase / Oxidoreductase
Similarity search - Component
Biological speciesShigella flexneri 2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsKim, Y. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Short Chain Dehydrogenase from Shigella flexneri
Authors: Kim, Y. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Short-chain dehydrogenase
B: Short-chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,66010
Polymers61,9952
Non-polymers6668
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-132 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.080, 133.200, 48.232
Angle α, β, γ (deg.)90.00, 104.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Short-chain dehydrogenase


Mass: 30997.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal 6 His tag with TEV protease cut site / Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Strain: 301 / Gene: yciK, S1358, SF1273 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q83RM3, UniProt: A0A0H2UYY2*PLUS

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Non-polymers , 5 types, 431 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Na Hepes pH 7.5, 1.5 ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→38.9 Å / Num. all: 53859 / Num. obs: 53859 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 7.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2716 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDphasing
RESOLVEphasing
Cootmodel building
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→38.8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2732 5.08 %RANDOM
Rwork0.155 ---
all0.156 53817 --
obs0.156 53817 98 %-
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.7639 Å2-0 Å25.4847 Å2
2---4.6549 Å2-0 Å2
3---1.891 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3977 0 35 423 4435
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.017
X-RAY DIFFRACTIONf_angle_d1.625
X-RAY DIFFRACTIONf_dihedral_angle_d18
LS refinement shellResolution: 1.7→1.73 Å
RfactorNum. reflection
Rfree0.24 132
Rwork0.216 -
obs-2534

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