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- PDB-5t5q: Crystal structure of Short-chain dehydrogenase/reductase SDR:Gluc... -

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Basic information

Entry
Database: PDB / ID: 5t5q
TitleCrystal structure of Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase from Brucella melitensis
ComponentsShort-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Brucella melitensis / Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase / BAB2_0029 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / nucleotide binding
Similarity search - Function
PKS_KR / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase from Brucella melitensis
Authors: Abendroth, J. / Phan, J.N. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionAug 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase
B: Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase
C: Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase
D: Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,99812
Polymers104,9164
Non-polymers3,0828
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19580 Å2
ΔGint-183 kcal/mol
Surface area28880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.850, 108.150, 65.660
Angle α, β, γ (deg.)90.000, 103.120, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1:2 and (name N or name...
21(chain B and (resid 1:3 or (resid 4 and (name...
31(chain C and ((resid 1:2 and (name N or name...
41(chain D and ((resid 1:2 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 1:2 and (name N or name...A1 - 2
121(chain A and ((resid 1:2 and (name N or name...A1 - 300
131(chain A and ((resid 1:2 and (name N or name...A1 - 300
141(chain A and ((resid 1:2 and (name N or name...A1 - 300
151(chain A and ((resid 1:2 and (name N or name...A1 - 300
211(chain B and (resid 1:3 or (resid 4 and (name...B1 - 3
221(chain B and (resid 1:3 or (resid 4 and (name...B4
231(chain B and (resid 1:3 or (resid 4 and (name...B1 - 300
241(chain B and (resid 1:3 or (resid 4 and (name...B1 - 300
251(chain B and (resid 1:3 or (resid 4 and (name...B1 - 300
261(chain B and (resid 1:3 or (resid 4 and (name...B1 - 300
311(chain C and ((resid 1:2 and (name N or name...C1 - 2
321(chain C and ((resid 1:2 and (name N or name...C1 - 300
331(chain C and ((resid 1:2 and (name N or name...C1 - 300
341(chain C and ((resid 1:2 and (name N or name...C1 - 300
351(chain C and ((resid 1:2 and (name N or name...C1 - 300
411(chain D and ((resid 1:2 and (name N or name...D1 - 2
421(chain D and ((resid 1:2 and (name N or name...D1 - 300
431(chain D and ((resid 1:2 and (name N or name...D1 - 300
441(chain D and ((resid 1:2 and (name N or name...D1 - 300
451(chain D and ((resid 1:2 and (name N or name...D1 - 300

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Components

#1: Protein
Short-chain dehydrogenase/reductase SDR:Glucose/ribitol dehydrogenase / BrabA.00010.d


Mass: 26228.975 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (strain 2308) (bacteria)
Strain: 2308 / Gene: BAB2_0029 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2YL80, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 42.5 % / Mosaicity: 0.187 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Molecular Dimensions Morpheus screen D12: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD; 20mM of each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, ...Details: Molecular Dimensions Morpheus screen D12: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD; 20mM of each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol; 0.1 M bicine/Trizma base pH 8.5; BrabA.00010.d.A1.PS00356 at 21.7 mg/ml+ 5mM NAD; cryo: direct; tray 272553d12, puck vkb7-2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 15, 2016 / Details: RIGAKU VARIMAX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 63730 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.6
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.95-20.4962.530.808198.7
2-2.060.4113.450.873199.5
2.06-2.120.3244.850.917199
2.12-2.180.276.250.95199.4
2.18-2.250.2148.260.97198.7
2.25-2.330.1999.160.979198.8
2.33-2.420.15911.870.987198.9
2.42-2.520.15812.710.99199.1
2.52-2.630.13214.790.992198.8
2.63-2.760.1116.910.995199
2.76-2.910.08620.90.997199.3
2.91-3.080.06924.890.998199.5
3.08-3.30.05629.860.999199.4
3.3-3.560.04437.760.999199.6
3.56-3.90.03547.950.999199.5
3.9-4.360.03250.060.999199.5
4.36-5.030.02955.840.999199.8
5.03-6.170.03250.330.999199.8
6.17-8.720.02955.060.999199.9
8.72-500.02566.760.999198.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata scaling
ARPmodel building
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2p68

2p68


Resolution: 1.95→50 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.06
RfactorNum. reflection% reflection
Rfree0.2187 2011 3.16 %
Rwork0.1745 --
obs0.1759 63727 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.48 Å2 / Biso mean: 37.6008 Å2 / Biso min: 12.16 Å2
Refinement stepCycle: final / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7019 0 212 441 7672
Biso mean--41.32 37.52 -
Num. residues----962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077399
X-RAY DIFFRACTIONf_angle_d0.9410089
X-RAY DIFFRACTIONf_chiral_restr0.0561185
X-RAY DIFFRACTIONf_plane_restr0.0061369
X-RAY DIFFRACTIONf_dihedral_angle_d11.4854485
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3927X-RAY DIFFRACTION8.114TORSIONAL
12B3927X-RAY DIFFRACTION8.114TORSIONAL
13C3927X-RAY DIFFRACTION8.114TORSIONAL
14D3927X-RAY DIFFRACTION8.114TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.99880.30051400.25524385452599
1.9988-2.05280.26831210.25434432455399
2.0528-2.11320.31421680.24694354452299
2.1132-2.18140.30441150.23474448456399
2.1814-2.25940.2811550.22224372452799
2.2594-2.34980.24981300.21064357448799
2.3498-2.45680.23971530.19294380453399
2.4568-2.58630.2721660.19334358452499
2.5863-2.74830.22941480.1864408455699
2.7483-2.96040.19121360.17674408454499
2.9604-3.25820.21471370.17594428456599
3.2582-3.72940.20061340.155844314565100
3.7294-4.69760.18271470.130544784625100
4.6976-41.29990.17491610.141944774638100
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)
12.03680.8124-0.00123.1391-0.07992.24130.010.1863-0.2723-0.30620.08510.67030.4938-0.4636-0.04410.3003-0.0768-0.02850.2545-0.08470.4834-11.92350.640776.5691
21.67630.47310.49142.09710.11721.87740.03040.0051-0.1886-0.0534-0.12170.16880.2024-0.03190.10430.19130.0280.05620.0846-0.02180.22753.15376.112785.6097
31.60590.12740.43351.5473-0.62412.00980.0137-0.03750.09510.0039-0.0940.3649-0.0449-0.14920.06510.14910.02990.01370.1351-0.03480.2344-1.582818.802677.6377
43.64070.14950.45162.0351-0.16974.62110.0110.74110.0841-0.95490.08550.30870.2477-0.2887-0.08850.55160.0979-0.10810.41870.03820.26240.179627.443951.9316
50.7320.1995-0.23791.6338-0.24121.20760.09980.48320.1954-0.4471-0.25020.0088-0.2390.16590.11640.37990.08760.01230.3370.11720.25419.96634.283761.9411
63.9067-1.1671-1.07263.91571.20262.49120.08070.5143-0.2107-0.5242-0.1433-0.20140.15420.38170.0590.31610.09470.03510.34420.01330.184210.748919.097164.8394
72.9596-0.4518-0.46112.80010.71971.90130.00910.4225-0.1505-0.4361-0.17790.14420.16510.10690.1420.24910.05980.00160.1915-0.00630.15056.135917.153166.5437
80.53090.22910.00210.4575-0.32220.7140.0057-0.0683-0.01310.2516-0.1991-0.364-0.05190.68720.09920.353-0.044-0.15630.7270.24960.35432.208813.4366101.5936
91.68880.2071.07540.41880.12161.29780.15590.0243-0.24880.1807-0.1849-0.41960.26830.6183-0.12750.37120.116-0.16790.7710.30150.378733.00574.3406105.0643
102.72810.35561.72261.2630.86421.42230.0703-0.0506-0.29710.4744-0.0816-0.43120.07590.6878-0.06910.49990.0768-0.15990.61770.20590.34129.09414.2886108.3608
112.44170.69470.89492.36791.3271.29360.0346-0.3941-0.12450.5568-0.1251-0.09070.09440.40950.11120.5715-0.0141-0.06640.46020.15580.249320.91145.8966112.6826
121.47390.1412-0.12622.0916-0.46581.29990.0354-0.0235-0.25390.2024-0.1778-0.12510.28630.48880.08260.24360.06950.02520.20890.07220.212317.0475.818793.8144
132.57420.62950.18653.14110.60131.80670.03540.0215-0.06520.2841-0.2301-0.14570.03590.42820.16620.21620.00060.00180.19350.08790.131817.036314.266892.6096
142.6224-1.65770.32645.9025-0.16545.43050.2448-0.1599-0.3210.09410.22-0.42530.26330.6217-0.40030.52960.1270.02650.67950.02420.638932.13843.16577.0735
152.0548-0.2859-1.22040.8235-0.6271.54660.0198-0.1169-0.10240.1652-0.3265-0.3866-0.07930.74460.19170.2078-0.0568-0.02570.49330.17640.302527.522418.718787.5424
161.23960.508-0.11680.25520.01310.09270.0637-0.08490.0940.0716-0.0375-0.0504-0.04660.12010.05640.4453-0.6291-0.20830.77340.31260.568935.692837.53690.1962
170.82470.11350.28790.48150.02030.60030.0898-0.16520.35250.2795-0.141-0.1801-0.21260.1630.15930.7135-0.5298-0.22580.77230.21590.723836.065247.459387.753
181.21810.2602-0.08460.5062-0.03070.5142-0.02310.0280.43870.0108-0.3911-0.4984-0.66770.657-0.18430.399-0.26240.0010.54760.33550.467526.771838.902276.4238
191.70060.261-0.23691.2618-0.15051.40380.1926-0.07310.5287-0.0351-0.2569-0.3005-0.64160.453-0.10150.3905-0.1443-0.0290.38040.14260.367522.490436.029985.9355
200.4387-0.5577-0.5045.0639-0.12920.71090.1307-0.06180.4620.1793-0.18810.2383-0.50040.17120.07920.5666-0.1136-00.2365-0.02450.34159.952337.569397.4467
211.43930.119-0.72790.1235-0.03071.0956-0.0333-0.06470.13650.1612-0.2984-0.2668-0.33140.7190.16080.29-0.1474-0.05080.46810.18350.297424.833327.416188.5198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 81 )A1 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 171 )A82 - 171
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 245 )A172 - 245
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 51 )B1 - 51
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 171 )B52 - 171
6X-RAY DIFFRACTION6chain 'B' and (resid 172 through 204 )B172 - 204
7X-RAY DIFFRACTION7chain 'B' and (resid 205 through 245 )B205 - 245
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 29 )C1 - 29
9X-RAY DIFFRACTION9chain 'C' and (resid 30 through 51 )C30 - 51
10X-RAY DIFFRACTION10chain 'C' and (resid 52 through 66 )C52 - 66
11X-RAY DIFFRACTION11chain 'C' and (resid 67 through 81 )C67 - 81
12X-RAY DIFFRACTION12chain 'C' and (resid 82 through 150 )C82 - 150
13X-RAY DIFFRACTION13chain 'C' and (resid 151 through 187 )C151 - 187
14X-RAY DIFFRACTION14chain 'C' and (resid 188 through 204 )C188 - 204
15X-RAY DIFFRACTION15chain 'C' and (resid 205 through 245 )C205 - 245
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 29 )D1 - 29
17X-RAY DIFFRACTION17chain 'D' and (resid 30 through 51 )D30 - 51
18X-RAY DIFFRACTION18chain 'D' and (resid 52 through 171 )D52 - 171
19X-RAY DIFFRACTION19chain 'D' and (resid 172 through 194 )D172 - 194
20X-RAY DIFFRACTION20chain 'D' and (resid 195 through 212 )D195 - 212
21X-RAY DIFFRACTION21chain 'D' and (resid 213 through 245 )D213 - 245

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