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- PDB-5iz4: Crystal structure of a putative short-chain dehydrogenase/reducta... -

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Basic information

Entry
Database: PDB / ID: 5iz4
TitleCrystal structure of a putative short-chain dehydrogenase/reductase from Burkholderia xenovorans
ComponentsPutative short-chain dehydrogenase/reductase
KeywordsOXIDOREDUCTASE / SSGCID / Burkholderia xenovorans / short-chain dehydrogenase/reductase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / nucleotide binding
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
ADENOSINE-5'-DIPHOSPHATE / Short-chain dehydrogenase/reductase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a putative short-chain dehydrogenase/reductase from Burkholderia xenovorans
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 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 1.2Sep 27, 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

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Assembly

Deposited unit
A: Putative short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0753
Polymers28,5291
Non-polymers5452
Water4,053225
1
A: Putative short-chain dehydrogenase/reductase
hetero molecules

A: Putative short-chain dehydrogenase/reductase
hetero molecules

A: Putative short-chain dehydrogenase/reductase
hetero molecules

A: Putative short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,29912
Polymers114,1174
Non-polymers2,1828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation15_455y-1/2,x+1/2,-z+1/21
crystal symmetry operation16_445-y-1/2,-x-1/2,-z+1/21
Buried area15620 Å2
ΔGint-73 kcal/mol
Surface area32630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.610, 84.610, 135.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-572-

HOH

21A-587-

HOH

31A-602-

HOH

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Components

#1: Protein Putative short-chain dehydrogenase/reductase / BuxeA.00010.e.B1


Mass: 28529.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_C0900 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13GL4, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytic Morpheus f12: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD; 20mM of each D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyld-glucosamine; 10mM bicine/Trizma ...Details: Microlytic Morpheus f12: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD; 20mM of each D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyld-glucosamine; 10mM bicine/Trizma base pH 8.5; BuxeA.00010.e.B1.PS37833 at 12.8mg/ml + 3mM NAD, direct cryo; tray: 270602f12, puck jra0-6; only the ADP moiety of NAD was observed in the density

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 17, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.75→35.865 Å / Num. obs: 25142 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 19.78 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.058 / Net I/σ(I): 30.22
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.75-1.80.5294.64199.9
1.8-1.840.415.93199.9
1.84-1.90.3437.311100
1.9-1.960.2719.221100
1.96-2.020.2111.831100
2.02-2.090.15715.371100
2.09-2.170.13417.931100
2.17-2.260.10922.34199.9
2.26-2.360.09225.711100
2.36-2.470.07630.31100
2.47-2.610.06535.1199.8
2.61-2.770.05440.87199.9
2.77-2.960.04646.99199.9
2.96-3.20.03756.781100
3.2-3.50.03165.591100
3.5-3.910.02772.831100
3.91-4.520.02678.45199.8
4.52-5.530.02579.311100
5.53-7.830.02975.23199.6
7.83-35.8650.02972.91196.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
MOLREPphasing
PHENIXdev_2356refinement
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4e3z

4e3z


Resolution: 1.75→35.865 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.58
RfactorNum. reflection% reflection
Rfree0.182 1900 7.57 %
Rwork0.1521 --
obs0.1543 25101 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84 Å2 / Biso mean: 26.3457 Å2 / Biso min: 11.44 Å2
Refinement stepCycle: final / Resolution: 1.75→35.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 35 227 2057
Biso mean--41.71 37.19 -
Num. residues----247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051927
X-RAY DIFFRACTIONf_angle_d0.7972645
X-RAY DIFFRACTIONf_chiral_restr0.053316
X-RAY DIFFRACTIONf_plane_restr0.005343
X-RAY DIFFRACTIONf_dihedral_angle_d14.491161
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 (%)
1.75-1.79380.25171340.187616171751100
1.7938-1.84230.2161150.175116521767100
1.8423-1.89650.21391500.169116061756100
1.8965-1.95770.23811390.173816281767100
1.9577-2.02760.22681350.167416251760100
2.0276-2.10880.21491350.158516341769100
2.1088-2.20480.19141340.153116611795100
2.2048-2.3210.17211510.148316051756100
2.321-2.46640.19741370.151616471784100
2.4664-2.65680.19681390.154716671806100
2.6568-2.9240.20051340.151516721806100
2.924-3.34690.16761330.144816801813100
3.3469-4.21560.15371330.131517011834100
4.2156-35.87270.14891310.15721806193799
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)
11.6811.16090.56723.27270.67892.6875-0.10150.13120.1303-0.34480.1063-0.061-0.41320.1899-0.00270.3005-0.0370.04240.1524-0.00030.1958-23.980820.120713.5878
22.5010.27590.17820.56480.1270.83090.00140.15150.0498-0.2210.0411-0.0558-0.0560.1151-0.04960.24990.00380.03750.10420.00090.1336-32.51457.577811.0594
34.0774-0.551-0.21080.8189-0.16931.0274-0.0809-0.14440.0217-0.06380.028-0.08980.01790.08610.05980.17660.00540.01020.1051-0.00340.1279-33.90944.680522.3599
42.3409-0.7784-0.71932.11030.53122.39980.09440.06850.2685-0.2496-0.05250.0188-0.2857-0.19360.00120.1690.0048-0.01550.1182-0.00240.1262-35.778415.431228.5959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 69 )A3 - 69
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 138 )A70 - 138
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 183 )A139 - 183
4X-RAY DIFFRACTION4chain 'A' and (resid 184 through 261 )A184 - 261

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