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- PDB-3iah: Crystal Structure of Short Chain Dehydrogenase (yciK) from Salmon... -

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Basic information

Entry
Database: PDB / ID: 3iah
TitleCrystal Structure of Short Chain Dehydrogenase (yciK) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 in Complex with NADP and Acetate.
ComponentsShort Chain Dehydrogenase yciK
KeywordsOXIDOREDUCTASE / Short Chain Dehydrogenase / NADP / Acetate / idp00971 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


: / oxidoreductase activity / nucleotide binding / cytosol
Similarity search - Function
short chain dehydrogenase / 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
ACETATE ION / ETHANOL / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative oxoacyl-(Acyl carrier protein) reductase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsMinasov, G. / Halavaty, A. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Short Chain Dehydrogenase (yciK) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 in Complex with NADP and Acetate.
Authors: Minasov, G. / Halavaty, A. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short Chain Dehydrogenase yciK
B: Short Chain Dehydrogenase yciK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,48210
Polymers57,6902
Non-polymers1,7928
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-33 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.664, 43.302, 71.916
Angle α, β, γ (deg.)90.00, 93.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Short Chain Dehydrogenase yciK / Putative oxoacyl-(Acyl carrier protein) reductase


Mass: 28845.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM1717, yciK / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q7CQG2

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Non-polymers , 5 types, 484 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein solution:0.3M NaCl, 10mM HEPES (pH 7.5); Screen solution: 0.2M Ammonium Acetate, 10mM NADP, 0.1M Bis-Tris (pH 5.5), 25% PEG 3350. , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 17, 2009 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.83→30 Å / Num. all: 43678 / Num. obs: 43678 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.5
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2180 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G1T

3g1t


Resolution: 1.83→27.43 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.767 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Individual Isotropic Temperature Factors Refined
Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17644 2183 5 %RANDOM
Rwork0.14327 ---
all0.14497 41212 --
obs0.14497 41212 99.87 %-
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 mean: 14.127 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å2-0 Å20.25 Å2
2--2.16 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.83→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3925 0 115 476 4516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224293
X-RAY DIFFRACTIONr_bond_other_d0.0010.022906
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9915857
X-RAY DIFFRACTIONr_angle_other_deg0.93537064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.2275539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.41823.687198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.16815720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4591541
X-RAY DIFFRACTIONr_chiral_restr0.0890.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214856
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02867
X-RAY DIFFRACTIONr_mcbond_it0.9451.52630
X-RAY DIFFRACTIONr_mcbond_other0.311.51060
X-RAY DIFFRACTIONr_mcangle_it1.66124233
X-RAY DIFFRACTIONr_scbond_it2.82831663
X-RAY DIFFRACTIONr_scangle_it4.494.51624
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 152 -
Rwork0.204 3013 -
obs-3013 99.94 %
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)
12.91290.047-0.90553.2222-0.61632.53730.11370.34650.4163-0.1548-0.02780.1105-0.3379-0.1731-0.08590.13950.0068-0.01060.13680.0850.08616.42324.69994.5343
22.69250.22631.60395.2521-3.04427.213-0.14480.66830.1041-0.85180.03060.38370.3082-0.1570.11430.2388-0.0373-0.05450.3428-0.0160.123412.551912.0084-0.7354
32.44080.3484-1.56410.4391-0.65793.1119-0.19640.2606-0.1362-0.20430.0733-0.02010.39140.05910.12310.1403-0.0106-0.00380.101-0.00750.066220.90329.0549.7921
41.5210.05380.00510.7386-0.31611.0526-0.03590.0410.19460.01180.03770.0558-0.1172-0.0677-0.00170.0625-0.0112-0.0120.03050.01540.066615.133618.30319.8131
53.0099-0.1134-0.42292.17190.2973.3584-0.0206-0.4649-0.07270.30540.0337-0.0016-0.0049-0.0086-0.01310.08290.0150.01140.08550.03480.047820.67190.771455.3156
62.9008-1.40340.23772.4837-1.19888.0937-0.1724-0.2601-0.33740.25410.175-0.0080.52760.2061-0.00260.18190.03460.02830.04190.05030.180424.9202-11.041948.0472
72.41671.1079-2.89060.7106-0.79914.8307-0.69140.356-0.3924-0.48690.1963-0.18230.5375-0.44030.49510.6326-0.08-0.04820.3267-0.01450.725311.9135-11.319435.6545
81.3203-0.01450.24250.5595-0.02891.0434-0.0401-0.0440.04940.02760.0192-0.0153-0.0391-0.06420.02090.04360.00950.00390.00670.00440.05621.74457.347740.5654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 43
2X-RAY DIFFRACTION2A44 - 72
3X-RAY DIFFRACTION3A73 - 108
4X-RAY DIFFRACTION4A109 - 253
5X-RAY DIFFRACTION5B1 - 40
6X-RAY DIFFRACTION6B41 - 72
7X-RAY DIFFRACTION7B73 - 85
8X-RAY DIFFRACTION8B86 - 253

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