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Basic information

Entry
Database: PDB / ID: 4da9
TitleCrystal structure of putative Short-chain dehydrogenase/reductase from Sinorhizobium meliloti 1021
ComponentsShort-chain dehydrogenase/reductase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / dehydrogenase/reductase / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(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
Similarity search - Domain/homology
Short-chain dehydrogenase/reductase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.5 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of putative Short-chain dehydrogenase/reductase from Sinorhizobium meliloti 1021
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C.
History
DepositionJan 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Other
Revision 1.2Nov 20, 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_ref_seq_dif / 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_ref_seq_dif.details / _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/reductase
B: Short-chain dehydrogenase/reductase
C: Short-chain dehydrogenase/reductase
D: Short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9398
Polymers118,5544
Non-polymers3844
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-161 kcal/mol
Surface area36270 Å2
MethodPISA
2
A: Short-chain dehydrogenase/reductase
D: Short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4694
Polymers59,2772
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-64 kcal/mol
Surface area20450 Å2
MethodPISA
3
A: Short-chain dehydrogenase/reductase
C: Short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4694
Polymers59,2772
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-52 kcal/mol
Surface area21110 Å2
MethodPISA
4
B: Short-chain dehydrogenase/reductase
C: Short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4694
Polymers59,2772
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-61 kcal/mol
Surface area20220 Å2
MethodPISA
5
B: Short-chain dehydrogenase/reductase
D: Short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4694
Polymers59,2772
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-56 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.333, 126.589, 127.093
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Short-chain dehydrogenase/reductase


Mass: 29638.588 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R03296, SMc04391 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: Q92L02, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Ammonium sulfate, 22% PEG 4000, 0.1M sodium acetate, pH 7.5, VAPOR DIFFUSION, SITTING 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: Nov 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 4.2 % / Av σ(I) over netI: 21.81 / Number: 322959 / Rmerge(I) obs: 0.074 / Χ2: 1.38 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 77562 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.78509910.0332.4474.3
5.386.7810010.0471.7944.2
4.75.3810010.0481.8254.1
4.274.710010.0562.2784.2
3.974.2799.910.0682.1854.2
3.733.9710010.0791.9594.2
3.553.7310010.0911.5994.2
3.393.5510010.1111.4264.2
3.263.3910010.1441.274.2
3.153.2610010.1831.1674.2
3.053.1510010.2381.0844.2
2.963.0510010.3081.0514.2
2.892.9610010.4031.0074.2
2.822.8910010.4720.964.1
2.752.8210010.6380.944.1
2.692.7510010.750.9294.1
2.642.6910010.8940.914.1
2.592.6410010.9044.1
2.542.5910010.914.1
2.52.5410010.8934.1
ReflectionResolution: 2.5→50 Å / Num. obs: 77562 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.074 / Χ2: 1.382 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.5-2.544.139030.8931100
2.54-2.594.138340.911100
2.59-2.644.139270.9041100
2.64-2.694.138800.9111000.894
2.69-2.754.138540.92911000.75
2.75-2.824.138880.9411000.638
2.82-2.894.138550.9611000.472
2.89-2.964.239001.00711000.403
2.96-3.054.238581.05111000.308
3.05-3.154.239031.08411000.238
3.15-3.264.238881.16711000.183
3.26-3.394.238731.2711000.144
3.39-3.554.238701.42611000.111
3.55-3.734.238921.59911000.091
3.73-3.974.238771.95911000.079
3.97-4.274.238482.185199.90.068
4.27-4.74.239022.27811000.056
4.7-5.384.138801.82511000.048
5.38-6.784.238691.79411000.047
6.78-504.338612.4471990.033

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-3000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.98 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.2151 / WRfactor Rwork: 0.1614 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8324 / SU B: 18.07 / SU ML: 0.189 / SU R Cruickshank DPI: 0.3263 / SU Rfree: 0.2421 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 2034 5 %RANDOM
Rwork0.177 ---
obs0.1797 40461 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 223.47 Å2 / Biso mean: 74.3428 Å2 / Biso min: 35.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6335 0 20 149 6504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196415
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.9738662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0245858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5523.137255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73515986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9941560
X-RAY DIFFRACTIONr_chiral_restr0.0860.21035
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214768
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 147 -
Rwork0.295 2560 -
all-2707 -
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)
11.5079-0.2540.61721.0172-0.50431.7899-0.05570.07880.16270.0866-0.0541-0.1475-0.12990.01220.10980.05170.0373-0.01990.08230.02660.042979.027339.628549.8767
21.7060.1462-0.07262.527-1.10850.6233-0.1189-0.03230.0423-0.40290.12370.16140.0872-0.0551-0.00480.32420.0165-0.11460.07330.02050.059859.432162.725213.3249
30.79220.59660.30111.91060.31871.8331-0.09980.11720.099-0.18290.03840.2489-0.1067-0.21810.06140.05170.0603-0.01750.19290.03090.056550.526737.349436.1916
40.61720.18450.04631.9995-0.52850.9536-0.1071-0.04890.0802-0.3874-0.2023-0.4641-0.02120.31730.30930.15390.02440.05620.15920.14910.232189.845260.238422.9117
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 253
2X-RAY DIFFRACTION2B3 - 256
3X-RAY DIFFRACTION3C0 - 253
4X-RAY DIFFRACTION4D1 - 254

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