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- PDB-3f5q: CRYSTAL STRUCTURE OF putative short chain dehydrogenase from Esch... -

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Basic information

Entry
Database: PDB / ID: 3f5q
TitleCRYSTAL STRUCTURE OF putative short chain dehydrogenase from Escherichia coli CFT073
Componentsdehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / dehydrogenase / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


Oxidoreductases / 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
Hypothetical oxidoreductase yciK / Hypothetical oxidoreductase yciK
Similarity search - Component
Biological speciesEscherichia coli O6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 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 an uncharacterized protein
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 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
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

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Assembly

Deposited unit
A: dehydrogenase
B: dehydrogenase


Theoretical massNumber of molelcules
Total (without water)58,3562
Polymers58,3562
Non-polymers00
Water6,521362
1
A: dehydrogenase

B: dehydrogenase


Theoretical massNumber of molelcules
Total (without water)58,3562
Polymers58,3562
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Buried area2950 Å2
ΔGint-22 kcal/mol
Surface area19280 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.412, 48.011, 65.232
Angle α, β, γ (deg.)100.290, 102.670, 105.260
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asymmetric unit.

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Components

#1: Protein dehydrogenase / Hypothetical oxidoreductase yciK


Mass: 29178.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6 (bacteria) / Strain: CFT073 / Gene: AAN80202.1, c1736, yciK / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: Q8FHV3, UniProt: A0A0H2V6Y9*PLUS, Oxidoreductases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 37.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M ammonium acetate, 0.1M HEPES, 25% PEG3350, pH 7.5, 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: 3.8 % / Av σ(I) over netI: 39.86 / Number: 158882 / Rmerge(I) obs: 0.087 / Χ2: 7.8 / D res high: 1.76 Å / D res low: 50 Å / Num. obs: 41952 / % possible obs: 94.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.795097.810.07319.8743.8
3.013.7993.110.07412.8163.8
2.633.0198.310.09312.0613.9
2.392.6398.110.1019.173.9
2.222.3980.410.117.2683.7
2.092.2297.210.1114.9483.9
1.982.099710.1253.6523.9
1.91.9895.410.1583.3433.7
1.821.996.110.1672.1063.8
1.761.8292.110.1921.7793.5
ReflectionResolution: 1.76→50 Å / Num. obs: 41952 / % possible obs: 94.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Χ2: 7.802 / Net I/σ(I): 39.862
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.76-1.823.50.19240781.779192.1
1.82-1.93.80.16742452.106196.1
1.9-1.983.70.15842293.343195.4
1.98-2.093.90.12543413.652197
2.09-2.223.90.11142914.948197.2
2.22-2.393.70.1135707.268180.4
2.39-2.633.90.10143479.17198.1
2.63-3.013.90.093438112.061198.3
3.01-3.793.80.074412312.816193.1
3.79-503.80.073434719.874197.8

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.75 / FOM acentric: 0.75 / FOM centric: 0 / Reflection: 41211 / Reflection acentric: 41211 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricReflectionReflection acentric
5-28.6180.950.9518411841
3.1-50.950.9555435543
2.5-3.10.880.8872707270
2.2-2.50.790.7965526552
1.9-2.20.670.671250112501
1.8-1.90.550.5575047504

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.872 / SU B: 4.872 / SU ML: 0.079 / SU R Cruickshank DPI: 0.127 / SU Rfree: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2085 5.1 %RANDOM
Rwork0.171 ---
obs0.173 41194 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: 66.7 Å2 / Biso mean: 16.04 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0.14 Å20.04 Å2
2---0.06 Å2-0.07 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.76→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 0 362 3906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223659
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9614962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64624.514175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04215635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3581531
X-RAY DIFFRACTIONr_chiral_restr0.1020.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212797
X-RAY DIFFRACTIONr_mcbond_it1.0693.52299
X-RAY DIFFRACTIONr_mcangle_it3.485503688
X-RAY DIFFRACTIONr_scbond_it7.58501360
X-RAY DIFFRACTIONr_scangle_it1.3464.51274
LS refinement shellResolution: 1.76→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 126 -
Rwork0.21 2726 -
all-2852 -
obs--100 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.60470.6328-0.14681.8822-0.12560.8350.0565-0.0834-0.04610.1818-0.0921-0.0713-0.0002-0.07110.0357-0.07080.0205-0.0248-0.01690.0043-0.034421.257233.679361.5851
21.05980.9017-0.10031.0805-0.13250.8671-0.24050.1971-0.0845-0.37390.1993-0.0637-0.1206-0.01610.04120.0601-0.03820.0246-0.0304-0.0189-0.05676.7966.176935.6299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 246
2X-RAY DIFFRACTION2B6 - 245

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