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- PDB-5u8p: Crystal structure of a short chain dehydrogenase from Burkholderi... -

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Basic information

Entry
Database: PDB / ID: 5u8p
TitleCrystal structure of a short chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NAD
ComponentsShort chain dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / structural genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / nucleotide binding / metal ion binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 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 / Uncharacterized oxidoreductase YghA
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a short chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NAD
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short chain dehydrogenase
B: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6076
Polymers65,2322
Non-polymers1,3754
Water14,124784
1
A: Short chain dehydrogenase
B: Short chain dehydrogenase
hetero molecules

A: Short chain dehydrogenase
B: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,21412
Polymers130,4634
Non-polymers2,7518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area20440 Å2
ΔGint-146 kcal/mol
Surface area32100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.160, 103.080, 87.000
Angle α, β, γ (deg.)90.000, 120.680, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-887-

HOH

21B-755-

HOH

31B-809-

HOH

41B-875-

HOH

51B-884-

HOH

61B-886-

HOH

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Components

#1: Protein Short chain dehydrogenase


Mass: 32615.799 Da / Num. of mol.: 2 / Fragment: residues 28-328
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAL1205 / Plasmid: BuceA.00010.v.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4EEE3
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus screen, D9: 10% w/v PEG 20 000, 20% v/v PEG MME 550: 20mM of each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol: 100mM bicine/Trizma ...Details: Morpheus screen, D9: 10% w/v PEG 20 000, 20% v/v PEG MME 550: 20mM of each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol: 100mM bicine/Trizma base pH 8.5: BuceA.00010.v.B2.PS01749 at 21.12 mg/ml + 4mM NAD: cryo: direct: tray 2486004d9, puck PLT0-10

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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: Nov 29, 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: 1.4→31.416 Å / Num. obs: 135756 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.179 % / Biso Wilson estimate: 8.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.071 / Χ2: 1.012 / Net I/σ(I): 15.73 / Num. measured all: 567351 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.443.6840.2964.52365001015099070.9110.34997.6
1.44-1.484.1660.2565.8640259987496640.9460.29497.9
1.48-1.524.220.2097.1139614956393880.9590.2498.2
1.52-1.574.2230.1718.2738933937692190.9750.19698.3
1.57-1.624.2280.159.3637501901288690.9790.17198.4
1.62-1.674.2310.12910.5536637876386590.9830.14898.8
1.67-1.744.2370.11112.0135283842683280.9870.12798.8
1.74-1.814.2390.09413.9434143812980540.990.10799.1
1.81-1.894.2380.08215.7532774780877330.9920.09499
1.89-1.984.2310.07118.0331358745674120.9940.08199.4
1.98-2.094.2320.06320.1329625703870010.9950.07299.5
2.09-2.214.2280.05722.1328442675667270.9950.06599.6
2.21-2.374.2220.05323.926498629762760.9950.0699.7
2.37-2.564.2260.04825.1924886590958890.9960.05699.7
2.56-2.84.2250.04626.5522640538053580.9960.05399.6
2.8-3.134.2270.04328.1120731492349050.9970.0599.6
3.13-3.614.220.0413018177432443070.9970.04699.6
3.61-4.434.1910.03931.0915310367136530.9970.04499.5
4.43-6.264.1740.03931.5411907287028530.9970.04599.4
6.26-31.4163.9470.03930.816133160115540.9970.04597.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2650)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JYD, native structure of same taraget

5jyd


Resolution: 1.4→31.416 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1373 2031 1.5 %
Rwork0.1167 133711 -
obs0.1171 135742 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.42 Å2 / Biso mean: 12.9912 Å2 / Biso min: 4.34 Å2
Refinement stepCycle: final / Resolution: 1.4→31.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 90 817 5213
Biso mean--6.87 27.15 -
Num. residues----584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084745
X-RAY DIFFRACTIONf_angle_d1.016557
X-RAY DIFFRACTIONf_chiral_restr0.082735
X-RAY DIFFRACTIONf_plane_restr0.007918
X-RAY DIFFRACTIONf_dihedral_angle_d16.2951842
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.43260.20991410.15148777891898
1.4326-1.46840.18831360.12918801893798
1.4684-1.50810.15121230.11468821894498
1.5081-1.55250.15811300.10538789891998
1.5525-1.60260.12361340.09758879901399
1.6026-1.65990.13591350.09398871900699
1.6599-1.72630.13121240.09668907903199
1.7263-1.80490.13121340.10068895902999
1.8049-1.90.11851490.10378900904999
1.9-2.0190.13981420.108689899131100
2.019-2.17490.12151480.112489589106100
2.1749-2.39370.12281040.11689969100100
2.3937-2.73990.13581500.12690009150100
2.7399-3.45130.14791320.131590409172100
3.4513-31.42360.13171490.124590889237100

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