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- PDB-5tt1: Crystal Structure of a Putative short-chain alcohol dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 5tt1
TitleCrystal Structure of a Putative short-chain alcohol dehydrogenase from Burkholderia multivorans
ComponentsPutative short-chain alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / short chain dehydrogenase/reductase family / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / penicillin binding / cell wall organization / nucleotide binding / plasma membrane
Similarity search - Function
: / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / short chain dehydrogenase / : ...: / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / short chain dehydrogenase / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Short-chain dehydrogenase/reductase SDR / Beta-lactamase/transpeptidase-like / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Penicillin-binding protein 1 / Short-chain alcohol dehydrogenase
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Putative short-chain alcohol dehydrogenase from Burkholderia multivorans
Authors: Dranow, D.M. / Abendroth, 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 / 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: Putative short-chain alcohol dehydrogenase
B: Putative short-chain alcohol dehydrogenase
C: Putative short-chain alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,04713
Polymers80,2903
Non-polymers75610
Water9,944552
1
A: Putative short-chain alcohol dehydrogenase
hetero molecules

A: Putative short-chain alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0358
Polymers53,5272
Non-polymers5086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4340 Å2
ΔGint-80 kcal/mol
Surface area17020 Å2
MethodPISA
2
B: Putative short-chain alcohol dehydrogenase
C: Putative short-chain alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0299
Polymers53,5272
Non-polymers5027
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-46 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.070, 53.190, 66.430
Angle α, β, γ (deg.)90.000, 89.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative short-chain alcohol dehydrogenase


Mass: 26763.496 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria)
Strain: ATCC 17616 / 249 / Gene: BMULJ_04988 / Plasmid: BumuA.00010.z.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KNM5, UniProt: A0A0H2WVW5*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BumuA.00010.z.B1.PS37887 at 25 mg/ml, mixed 1:1 with an equal volume Morpheus(c2): 10% (w/v) PEG-8000, 20% (v/v) ethylene glycol, 0.1 M MES/imidazole, pH=6.5, 0.03 M each sodium nitrate, ...Details: BumuA.00010.z.B1.PS37887 at 25 mg/ml, mixed 1:1 with an equal volume Morpheus(c2): 10% (w/v) PEG-8000, 20% (v/v) ethylene glycol, 0.1 M MES/imidazole, pH=6.5, 0.03 M each sodium nitrate, disodium hydrogen phosphate, and ammonium sulfate

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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: Jun 22, 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: 1.8→50 Å / Num. obs: 61331 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 20.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2% possible all
1.8-1.850.4892.54172000.82899.3
1.85-1.90.4192.980.88499.4
1.9-1.950.2674.70.9795.3
1.95-2.010.2425.220.94799.3
2.01-2.080.1836.710.96999.6
2.08-2.150.1558.010.97799.8
2.15-2.230.139.230.98499.5
2.23-2.320.09312.180.9997.6
2.32-2.430.08613.180.99199.9
2.43-2.550.07615.080.99399.8
2.55-2.680.06616.950.99399.8
2.68-2.850.057190.99599.8
2.85-3.040.05121.430.99699.9
3.04-3.290.04524.40.99699.9
3.29-3.60.0427.010.99799.7
3.6-4.020.04128.130.99699.2
4.02-4.650.03830.110.99799.8
4.65-5.690.03729.960.99699.9
5.69-8.050.03829.530.99799.6
8.050.03730.550.99797.8

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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: 5IDQ

5idq


Resolution: 1.8→40.619 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.61
RfactorNum. reflection% reflection
Rfree0.2076 2067 3.39 %
Rwork0.1763 --
obs0.1774 60968 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.44 Å2 / Biso mean: 27.7366 Å2 / Biso min: 9.81 Å2
Refinement stepCycle: final / Resolution: 1.8→40.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4917 0 44 558 5519
Biso mean--55.39 35.7 -
Num. residues----658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065115
X-RAY DIFFRACTIONf_angle_d0.8266954
X-RAY DIFFRACTIONf_chiral_restr0.055808
X-RAY DIFFRACTIONf_plane_restr0.005916
X-RAY DIFFRACTIONf_dihedral_angle_d15.1893108
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84180.27461250.22163950407599
1.8418-1.88790.28441330.216439384071100
1.8879-1.9390.45081100.37883530364089
1.939-1.9960.26041350.21293887402299
1.996-2.06040.22431380.199339694107100
2.0604-2.13410.26141460.184239644110100
2.1341-2.21950.24111520.18139084060100
2.2195-2.32050.31521140.2563789390395
2.3205-2.44280.18611480.169839534101100
2.4428-2.59590.21721350.173539764111100
2.5959-2.79630.22971260.177639864112100
2.7963-3.07760.22971370.175839874124100
3.0776-3.52270.18541680.162939814149100
3.5227-4.43730.15531450.13924005415099
4.4373-40.62920.15811550.139740784233100
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)
13.7250.3681-0.12284.2977-0.31471.4283-0.00750.12950.1079-0.0421-0.08640.3047-0.0764-0.19190.08170.20920.0499-0.00660.17660.00760.1379-18.9595-4.008412.1395
26.2473-0.82270.45782.5280.60181.30490.14070.074-0.1897-0.273-0.051-0.0209-0.0079-0.106-0.10810.23930.01620.01190.19870.00490.1194-10.2963-10.833110.5325
31.0183-0.38540.8120.8495-0.0521.4119-0.07080.08230.2783-0.0773-0.0614-0.0088-0.2724-0.06890.07630.21660.0143-0.01110.11640.01930.2065-6.21552.485723.9702
44.00641.22040.19143.01270.70043.0963-0.01590.328-0.3337-0.09660.088-0.06980.3996-0.0684-0.06060.2292-0.0099-0.00970.21530.01160.1267-34.080420.3837.4228
50.91160.12791.39880.25290.36982.50290.27010.1776-0.0816-0.1638-0.10970.03690.79360.1608-0.16790.30110.02280.0160.2020.01990.2033-29.824621.522221.8526
61.70420.4526-0.00190.5540.42351.89650.0107-0.0411-0.03280.0521-0.02390.16340.1754-0.2702-0.00430.1544-0.02040.02210.14290.00270.1615-37.848326.346424.891
73.03950.81860.40484.27082.47131.9311-0.0021-0.44110.16810.08670.0049-0.3105-0.16830.09840.04710.290.07710.00360.36520.03030.1924-17.096232.777958.909
82.56210.1569-0.1912.69510.41971.5666-0.0802-0.24720.07940.06370.1062-0.23520.0580.4365-0.02770.2120.0228-0.00920.29420.00740.1312-12.361834.730754.9413
91.4905-0.21580.43120.9102-0.50493.0364-0.0333-0.1318-0.05380.12550.01820.05360.0721-0.01660.02220.15390.00470.01740.1064-0.00180.11-24.638230.24141.4916
103.65430.00380.8561.67091.40972.8375-0.1107-0.51970.1190.1705-0.09960.12210.0434-0.4480.18220.21970.02540.04770.2879-0.0050.1329-33.150633.489252.575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 54 )A8 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 78 )A55 - 78
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 237 )A79 - 237
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 78 )B7 - 78
5X-RAY DIFFRACTION5chain 'B' and (resid 79 through 106 )B79 - 106
6X-RAY DIFFRACTION6chain 'B' and (resid 107 through 237 )B107 - 237
7X-RAY DIFFRACTION7chain 'C' and (resid 6 through 18 )C6 - 18
8X-RAY DIFFRACTION8chain 'C' and (resid 19 through 78 )C19 - 78
9X-RAY DIFFRACTION9chain 'C' and (resid 79 through 177 )C79 - 177
10X-RAY DIFFRACTION10chain 'C' and (resid 178 through 237 )C178 - 237

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