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- PDB-8ro4: The crystal structure of 2-hydroxy-3-keto-glucal hydratase AtHYD ... -

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Basic information

Entry
Database: PDB / ID: 8ro4
TitleThe crystal structure of 2-hydroxy-3-keto-glucal hydratase AtHYD from A. tumefaciens
Components2-hydroxy-3-keto-glucal hydratase
KeywordsLYASE / hydratase
Function / homology:
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsGrininger, C. / Bitter, J. / Pfeiffer, M. / Nidetzky, B. / Pavkov-Keller, T.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundDOC 130 Austria
Austrian Science Funddoc.funds46 Austria
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Enzyme Machinery for Bacterial Glucoside Metabolism through a Conserved Non-hydrolytic Pathway.
Authors: Kastner, K. / Bitter, J. / Pfeiffer, M. / Grininger, C. / Oberdorfer, G. / Pavkov-Keller, T. / Weber, H. / Nidetzky, B.
History
DepositionJan 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification
Revision 1.2Oct 30, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-hydroxy-3-keto-glucal hydratase
C: 2-hydroxy-3-keto-glucal hydratase
D: 2-hydroxy-3-keto-glucal hydratase
B: 2-hydroxy-3-keto-glucal hydratase
E: 2-hydroxy-3-keto-glucal hydratase
F: 2-hydroxy-3-keto-glucal hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,61012
Polymers234,2806
Non-polymers3306
Water59433
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.320, 165.550, 93.380
Angle α, β, γ (deg.)90.000, 113.340, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 17 or resid 19...
d_2ens_1(chain "B" and (resid 2 through 17 or resid 19...
d_3ens_1(chain "C" and (resid 2 through 17 or resid 19...
d_4ens_1(chain "D" and (resid 2 through 17 or resid 19...
d_5ens_1(chain "E" and (resid 2 through 17 or resid 19...
d_6ens_1(chain "F" and (resid 2 through 17 or resid 19...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSASPASPAA2 - 172 - 17
d_12ALAALAPROPROAA19 - 4519 - 45
d_13LEULEULEULEUAA47 - 5047 - 50
d_14LYSLYSGLYGLYAA52 - 6552 - 65
d_15LEULEUALAALAAA67 - 6867 - 68
d_16THRTHRLEULEUAA70 - 10470 - 104
d_17GLYGLYGLYGLYAA106106
d_18PROPROPROPROAA108108
d_19ALAALAGLNGLNAA110 - 112110 - 112
d_110TRPTRPALAALAAA114 - 123114 - 123
d_111ALAALALEULEUAA125 - 131125 - 131
d_112SERSERPROPROAA133 - 150133 - 150
d_113ARGARGVALVALAA152 - 157152 - 157
d_114METMETGLUGLUAA159 - 176159 - 176
d_115ASNASNLEULEUAA178 - 202178 - 202
d_116ALAALAHISHISAA204 - 235204 - 235
d_117ARGARGPROPROAA237 - 307237 - 307
d_118ASPASPALAALAAA309 - 311309 - 311
d_119GLUGLUILEILEAA313 - 318313 - 318
d_120ASNASNASNASNAA320 - 343320 - 343
d_121ARGARGGLYGLYAA345 - 348345 - 348
d_21LYSLYSASPASPBD2 - 172 - 17
d_22ALAALAPROPROBD19 - 4519 - 45
d_23LEULEULEULEUBD47 - 5047 - 50
d_24LYSLYSGLYGLYBD52 - 6552 - 65
d_25LEULEUALAALABD67 - 6867 - 68
d_26THRTHRLEULEUBD70 - 10470 - 104
d_27GLYGLYGLYGLYBD106106
d_28PROPROPROPROBD108108
d_29ALAALAGLNGLNBD110 - 112110 - 112
d_210TRPTRPALAALABD114 - 123114 - 123
d_211ALAALALEULEUBD125 - 131125 - 131
d_212SERSERPROPROBD133 - 150133 - 150
d_213ARGARGVALVALBD152 - 157152 - 157
d_214METMETGLUGLUBD159 - 176159 - 176
d_215ASNASNLEULEUBD178 - 202178 - 202
d_216ALAALAHISHISBD204 - 235204 - 235
d_217ARGARGPROPROBD237 - 307237 - 307
d_218ASPASPALAALABD309 - 311309 - 311
d_219GLUGLUILEILEBD313 - 318313 - 318
d_220ASNASNASNASNBD320 - 343320 - 343
d_221ARGARGGLYGLYBD345 - 348345 - 348
d_31LYSLYSASPASPCB2 - 172 - 17
d_32ALAALAPROPROCB19 - 4519 - 45
d_33LEULEULEULEUCB47 - 5047 - 50
d_34LYSLYSGLYGLYCB52 - 6552 - 65
d_35LEULEUALAALACB67 - 6867 - 68
d_36THRTHRLEULEUCB70 - 10470 - 104
d_37GLYGLYGLYGLYCB106106
d_38PROPROPROPROCB108108
d_39ALAALAGLNGLNCB110 - 112110 - 112
d_310TRPTRPALAALACB114 - 123114 - 123
d_311ALAALALEULEUCB125 - 131125 - 131
d_312SERSERPROPROCB133 - 150133 - 150
d_313ARGARGVALVALCB152 - 157152 - 157
d_314METMETGLUGLUCB159 - 176159 - 176
d_315ASNASNLEULEUCB178 - 202178 - 202
d_316ALAALAHISHISCB204 - 235204 - 235
d_317ARGARGPROPROCB237 - 307237 - 307
d_318ASPASPALAALACB309 - 311309 - 311
d_319GLUGLUILEILECB313 - 318313 - 318
d_320ASNASNASNASNCB320 - 343320 - 343
d_321ARGARGGLYGLYCB345 - 348345 - 348
d_41LYSLYSASPASPDC2 - 172 - 17
d_42ALAALAPROPRODC19 - 4519 - 45
d_43LEULEULEULEUDC47 - 5047 - 50
d_44LYSLYSGLYGLYDC52 - 6552 - 65
d_45LEULEUALAALADC67 - 6867 - 68
d_46THRTHRLEULEUDC70 - 10470 - 104
d_47GLYGLYGLYGLYDC106106
d_48PROPROPROPRODC108108
d_49ALAALAGLNGLNDC110 - 112110 - 112
d_410TRPTRPALAALADC114 - 123114 - 123
d_411ALAALALEULEUDC125 - 131125 - 131
d_412SERSERPROPRODC133 - 150133 - 150
d_413ARGARGVALVALDC152 - 157152 - 157
d_414METMETGLUGLUDC159 - 176159 - 176
d_415ASNASNLEULEUDC178 - 202178 - 202
d_416ALAALAHISHISDC204 - 235204 - 235
d_417ARGARGPROPRODC237 - 307237 - 307
d_418ASPASPALAALADC309 - 311309 - 311
d_419GLUGLUILEILEDC313 - 318313 - 318
d_420ASNASNASNASNDC320 - 343320 - 343
d_421ARGARGGLYGLYDC345 - 348345 - 348
d_51LYSLYSASPASPEE2 - 172 - 17
d_52ALAALAPROPROEE19 - 4519 - 45
d_53LEULEULEULEUEE47 - 5047 - 50
d_54LYSLYSGLYGLYEE52 - 6552 - 65
d_55LEULEUALAALAEE67 - 6867 - 68
d_56THRTHRLEULEUEE70 - 10470 - 104
d_57GLYGLYGLYGLYEE106106
d_58PROPROPROPROEE108108
d_59ALAALAGLNGLNEE110 - 112110 - 112
d_510TRPTRPALAALAEE114 - 123114 - 123
d_511ALAALALEULEUEE125 - 131125 - 131
d_512SERSERPROPROEE133 - 150133 - 150
d_513ARGARGVALVALEE152 - 157152 - 157
d_514METMETGLUGLUEE159 - 176159 - 176
d_515ASNASNLEULEUEE178 - 202178 - 202
d_516ALAALAHISHISEE204 - 235204 - 235
d_517ARGARGPROPROEE237 - 307237 - 307
d_518ASPASPALAALAEE309 - 311309 - 311
d_519GLUGLUILEILEEE313 - 318313 - 318
d_520ASNASNASNASNEE320 - 343320 - 343
d_521ARGARGGLYGLYEE345 - 348345 - 348
d_61LYSLYSASPASPFF2 - 172 - 17
d_62ALAALAPROPROFF19 - 4519 - 45
d_63LEULEULEULEUFF47 - 5047 - 50
d_64LYSLYSGLYGLYFF52 - 6552 - 65
d_65LEULEUALAALAFF67 - 6867 - 68
d_66THRTHRLEULEUFF70 - 10470 - 104
d_67GLYGLYGLYGLYFF106106
d_68PROPROPROPROFF108108
d_69ALAALAGLNGLNFF110 - 112110 - 112
d_610TRPTRPALAALAFF114 - 123114 - 123
d_611ALAALALEULEUFF125 - 131125 - 131
d_612SERSERPROPROFF133 - 150133 - 150
d_613ARGARGVALVALFF152 - 157152 - 157
d_614METMETGLUGLUFF159 - 176159 - 176
d_615ASNASNLEULEUFF178 - 202178 - 202
d_616ALAALAHISHISFF204 - 235204 - 235
d_617ARGARGPROPROFF237 - 307237 - 307
d_618ASPASPALAALAFF309 - 311309 - 311
d_619GLUGLUILEILEFF313 - 318313 - 318
d_620ASNASNASNASNFF320 - 343320 - 343
d_621ARGARGGLYGLYFF345 - 348345 - 348

NCS oper:
IDCodeMatrixVector
1given(-0.854410088099, -0.428205537944, -0.294318566572), (-0.434629754216, 0.278568680796, 0.856444082722), (-0.284746164337, 0.859674070421, -0.424122758811)42.9672901629, -7.04701874404, 32.1364900215
2given(0.872608106949, 0.341800004607, 0.348895182738), (0.466257335123, -0.37020270502, -0.803463785518), (-0.145461985174, 0.863783951024, -0.482408640908)-15.3057290514, 44.4205567846, 31.9727734636
3given(-0.993609911702, 0.0096657788316, -0.112454062119), (0.00303961660883, -0.993673487085, -0.112266476723), (-0.112827762977, -0.111890901259, 0.987294445501)30.9145477621, 41.0100246257, 4.1229868915
4given(-0.90421503787, -0.377909928526, 0.198945347297), (-0.375342582858, 0.480957676333, -0.792336834351), (0.203747664485, -0.791115541181, -0.57673485218)27.3592277018, 39.570494467, 61.0355861939
5given(0.877443338343, 0.460255708169, -0.135121689955), (0.333227085965, -0.382239686696, 0.861888931994), (0.345040428324, -0.801284908764, -0.488763335174)-2.6377334716, -5.36404170515, 56.5023650867

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Components

#1: Protein
2-hydroxy-3-keto-glucal hydratase


Mass: 39046.715 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: JCSG+, condition G4 (0.2 M Trimethylamine N-oxide, 0.1M Tris pH 8.5, 20% w/vPEG 2000 MME) Protein buffer: 10 mM HEPES pH 7.0, 150 mM NaCl, 0.1 mM TCEP, 0.1 mM MnCl2 0.5 ul screen condition + ...Details: JCSG+, condition G4 (0.2 M Trimethylamine N-oxide, 0.1M Tris pH 8.5, 20% w/vPEG 2000 MME) Protein buffer: 10 mM HEPES pH 7.0, 150 mM NaCl, 0.1 mM TCEP, 0.1 mM MnCl2 0.5 ul screen condition + 0.5 ul protein solution (7.5 mg/ml)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0121 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: May 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0121 Å / Relative weight: 1
ReflectionResolution: 2.51→48.04 Å / Num. obs: 76408 / % possible obs: 97.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 63.78 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.114 / Net I/σ(I): 8.01
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 7125 / CC1/2: 0.61 / Rrim(I) all: 0.93 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSFeb 5, 2021data reduction
XSCALEdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→48.04 Å / SU ML: 0.3885 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.1342
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2173 2100 2.75 %
Rwork0.1807 74304 -
obs0.1817 76404 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.4 Å2
Refinement stepCycle: LAST / Resolution: 2.51→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16063 0 6 33 16102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002516519
X-RAY DIFFRACTIONf_angle_d0.547722399
X-RAY DIFFRACTIONf_chiral_restr0.04332296
X-RAY DIFFRACTIONf_plane_restr0.00452966
X-RAY DIFFRACTIONf_dihedral_angle_d13.47055898
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.479000962529
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.547113385988
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.489893378487
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.540086995819
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.52969872192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.570.4181250.36484423X-RAY DIFFRACTION87.36
2.57-2.640.38891410.30774987X-RAY DIFFRACTION99.4
2.64-2.710.31331410.27344998X-RAY DIFFRACTION99.32
2.71-2.790.3321410.24494997X-RAY DIFFRACTION99.3
2.79-2.880.2781420.23265019X-RAY DIFFRACTION99.23
2.88-2.980.31251410.24084990X-RAY DIFFRACTION98.96
2.98-3.10.30731390.25484923X-RAY DIFFRACTION97.29
3.1-3.240.30291400.22874954X-RAY DIFFRACTION97.96
3.24-3.410.27381420.20925005X-RAY DIFFRACTION99.5
3.41-3.620.22541420.18645036X-RAY DIFFRACTION99.31
3.62-3.90.21051410.17375013X-RAY DIFFRACTION99.08
3.9-4.30.18561410.15014980X-RAY DIFFRACTION98.65
4.3-4.920.1561390.13974913X-RAY DIFFRACTION96.5
4.92-6.190.17241420.15215009X-RAY DIFFRACTION99.02
6.19-48.040.17331430.14735057X-RAY DIFFRACTION98.21

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