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- PDB-5tt0: Crystal Structure of an Oxidoreductase (short chain dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 5tt0
TitleCrystal Structure of an Oxidoreductase (short chain dehydrogenase/reductase family) from Burkholderia thailandensis
ComponentsOxidoreductase, short chain dehydrogenase/reductase family
KeywordsOXIDOREDUCTASE / SSGCID / short chain dehydrogenase/reductase family / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
: / 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
Oxidoreductase, short chain dehydrogenase/reductase family
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of an Oxidoreductase (short chain dehydrogenase/reductase family) from Burkholderia thailandensis
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionOct 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
Revision 1.2Oct 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidoreductase, short chain dehydrogenase/reductase family
B: Oxidoreductase, short chain dehydrogenase/reductase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,62127
Polymers54,9382
Non-polymers1,68325
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-69 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.690, 109.080, 73.530
Angle α, β, γ (deg.)90.000, 99.650, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-568-

HOH

21B-561-

HOH

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Components

#1: Protein Oxidoreductase, short chain dehydrogenase/reductase family / Short chain dehydrogenase family protein


Mass: 27469.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264) (bacteria)
Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: BTH_II1195, DR63_4586 / Plasmid: ButhA.00010.z.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T608
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ButhA.00010.z.B1.PS02557 at 3.46 mg/ml, mixed 1:1 with an equal volume MCSG1(g5): 0.1 M Bis-Tris:HCl, pH=6.5, 2.0 M ammonium sulfate, cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 6, 2016 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 50699 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 16.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2% possible all
1.7-1.740.5062.66141620.854100
1.74-1.790.4143.320.876100
1.79-1.840.3483.980.91899.6
1.84-1.90.2874.820.94599.8
1.9-1.960.2126.40.96699.9
1.96-2.030.1737.940.97599.6
2.03-2.110.1310.130.98699.7
2.11-2.190.1111.870.98999.7
2.19-2.290.0914.270.99399.6
2.29-2.40.07716.520.99599.5
2.4-2.530.06918.270.99599.7
2.53-2.690.06120.50.99699.5
2.69-2.870.04924.410.99799.4
2.87-3.10.03928.940.99899.4
3.1-3.40.03333.950.99899.1
3.4-3.80.02738.740.99999.1
3.8-4.390.02443.710.99999.3
4.39-5.380.02245.230.99999.4
5.38-7.60.02444.890.99999.3
7.60.02249.90.99998.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX(1.11_2563)refinement
PDB_EXTRACT3.2data extraction
MoRDaphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JC8

5jc8


Resolution: 1.7→45.428 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.93
RfactorNum. reflection% reflection
Rfree0.1923 2023 3.99 %
Rwork0.1615 --
obs0.1627 50686 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.36 Å2 / Biso mean: 22.1227 Å2 / Biso min: 4.94 Å2
Refinement stepCycle: final / Resolution: 1.7→45.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3593 0 114 386 4093
Biso mean--42.35 24.6 -
Num. residues----505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053772
X-RAY DIFFRACTIONf_angle_d0.7345125
X-RAY DIFFRACTIONf_chiral_restr0.051620
X-RAY DIFFRACTIONf_plane_restr0.006663
X-RAY DIFFRACTIONf_dihedral_angle_d10.5522232
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 (%)
1.7-1.74250.24421390.22134453584100
1.7425-1.78960.23331470.198134823629100
1.7896-1.84230.23821520.188334803632100
1.8423-1.90180.25521400.17734343574100
1.9018-1.96970.20841500.162934923642100
1.9697-2.04860.19321470.160134983645100
2.0486-2.14180.19081360.149234753611100
2.1418-2.25470.18171430.152334483591100
2.2547-2.3960.18241620.15723463362599
2.396-2.5810.21541480.164934783626100
2.581-2.84070.19711460.16563484363099
2.8407-3.25160.19491460.15433449359599
3.2516-4.09630.14831190.13913513363299
4.0963-45.44460.18211480.16963522367099
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)
11.66720.5062-0.63191.3914-0.04622.03270.03580.02060.22-0.11510.04710.0412-0.3896-0.046-0.03780.17480.01070.00040.07520.00990.083428.48723.758111.8541
21.2870.15230.49920.3227-0.36332.58580.08810.07170.1499-0.0169-0.0136-0.0529-0.26310.0244-0.02060.11040.01120.02110.07020.00330.086126.46390.364428.6221
30.5753-0.4103-0.40641.7513-0.04741.6070.00270.09370.1277-0.0562-0.0192-0.2341-0.23560.23780.00160.0961-0.01360.01480.09530.02480.069327.6533-5.465127.091
40.603-0.58450.00161.0982-0.6981.8665-0.0067-0.01820.0828-0.0059-0.1059-0.22160.05810.34440.08190.1040.00750.00170.10390.0010.107937.9372-17.068226.6671
51.83190.03410.1911.39110.39842.29-0.004-0.0555-0.2449-0.1118-0.02690.00450.53750.00590.00520.2592-0.02330.01960.0947-0.010.104626.9125-39.022811.3418
62.2041-0.2966-1.80390.37530.23092.2085-0.0991-0.0248-0.07020.00070.00560.01910.325-0.00880.08530.188-0.0109-0.00840.0781-0.01540.094223.7047-35.914628.1453
70.3631-0.4431-0.56381.1250.051.1745-0.01050.0832-0.0787-0.0634-0.02730.16010.1737-0.21050.00650.1115-0.0323-0.01610.0877-0.01220.076820.1492-24.754622.6293
83.4105-3.0813-0.94847.8269-1.2644.50680.03620.49860.5587-0.30420.12430.4266-0.4434-0.59840.02970.1281-0.0053-0.04290.34030.060.22022.6803-8.455831.0457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 80 )A2 - 80
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 142 )A81 - 142
3X-RAY DIFFRACTION3chain 'A' and (resid 143 through 189 )A143 - 189
4X-RAY DIFFRACTION4chain 'A' and (resid 190 through 255 )A190 - 255
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 80 )B2 - 80
6X-RAY DIFFRACTION6chain 'B' and (resid 81 through 142 )B81 - 142
7X-RAY DIFFRACTION7chain 'B' and (resid 143 through 242 )B143 - 242
8X-RAY DIFFRACTION8chain 'B' and (resid 243 through 255 )B243 - 255

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