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- PDB-3f5s: CRYSTAL STRUCTURE OF putatitve short chain dehydrogenase from Shi... -

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Basic information

Entry
Database: PDB / ID: 3f5s
TitleCRYSTAL STRUCTURE OF putatitve short chain dehydrogenase from Shigella flexneri 2a str. 301
Componentsdehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC / dehydrogenase / PSI-2
Function / homology
Function and homology information


oxidoreductase activity / nucleotide 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.36 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putatitve short chain dehydrogenase from Shigella flexneri 2a str. 301
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionNov 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dehydrogenase
B: dehydrogenase


Theoretical massNumber of molelcules
Total (without water)56,7272
Polymers56,7272
Non-polymers00
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-23 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.993, 67.414, 65.031
Angle α, β, γ (deg.)90.000, 108.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein dehydrogenase /


Mass: 28363.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 2a str. 301 / Gene: AAP16771.1, S1358, SF1273, yciK / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q83RM3, UniProt: A0A0H2UYY2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.1M tris-hcl, 0.2 sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 25.92 / Number: 652231 / Rmerge(I) obs: 0.064 / Χ2: 1.58 / D res high: 1.34 Å / D res low: 50 Å / Num. obs: 184342 / % possible obs: 94.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.895094.710.0382.8363.6
2.292.8999.410.0492.5653.7
22.2991.510.0622.1363.6
1.82298.310.0851.6963.7
1.691.8298.110.1171.2073.8
1.591.6997.810.1641.093.8
1.511.5997.310.2341.0243.8
1.441.5196.510.3170.9873.5
1.391.4491.410.4080.9413
1.341.3977.710.4520.9282.5
ReflectionResolution: 1.34→50 Å / Num. obs: 184342 / % possible obs: 94.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.064 / Χ2: 1.583 / Net I/σ(I): 25.921
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.34-1.392.50.452152580.928177.7
1.39-1.4430.408178120.941191.4
1.44-1.513.50.317188530.987196.5
1.51-1.593.80.234191061.024197.3
1.59-1.693.80.164190641.09197.8
1.69-1.823.80.117191411.207198.1
1.82-23.70.085192851.696198.3
2-2.293.60.062178362.136191.5
2.29-2.893.70.049194652.565199.4
2.89-503.60.038185222.836194.7

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Phasing

Phasing dmFOM : 0.66 / FOM acentric: 0.67 / FOM centric: 0.57 / Reflection: 92307 / Reflection acentric: 90023 / Reflection centric: 2284
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
3.8-28.1440.930.940.8142183907311
2.4-3.80.90.90.751287012379491
1.9-2.40.810.810.621566015242418
1.7-1.90.680.690.481617415831343
1.4-1.70.550.550.372799627507489
1.3-1.40.430.440.311538915157232

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
SHELXSphasing
RefinementResolution: 1.36→7.99 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.884 / SU B: 1.679 / SU ML: 0.034 / SU R Cruickshank DPI: 0.06 / SU Rfree: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 4452 5 %RANDOM
Rwork0.184 ---
obs0.185 88705 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 15.753 Å2 / Biso min: 4.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.36→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 0 251 3770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223652
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9584958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0135466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23224.091176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16415641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9641535
X-RAY DIFFRACTIONr_chiral_restr0.0970.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212781
X-RAY DIFFRACTIONr_mcbond_it1.1173.52277
X-RAY DIFFRACTIONr_mcangle_it3.063503664
X-RAY DIFFRACTIONr_scbond_it5.864501375
X-RAY DIFFRACTIONr_scangle_it1.6564.51287
LS refinement shellResolution: 1.36→1.394 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 298 -
Rwork0.251 5349 -
all-5647 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9592-0.1227-0.12760.11260.03890.5642-0.00570.1581-0.0252-0.0242-0.01570.0125-0.04740.01650.0214-0.0083-0.0062-0.0027-0.0119-0.0027-0.015811.451928.281516.4093
20.80240.1613-0.20080.2525-0.01370.32740.0028-0.1062-0.02420.0447-0.0296-0.0241-0.0154-0.01650.0267-0.00590.0038-0.0046-0.00710.0024-0.0259-11.1927.795542.1601
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 241
2X-RAY DIFFRACTION2B5 - 242

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