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- PDB-7obu: Crystal structure of holo-F210W mutant of Hydroxy ketone aldolase... -

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Basic information

Entry
Database: PDB / ID: 7obu
TitleCrystal structure of holo-F210W mutant of Hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1, with the active site in the resting and the active state
ComponentsHpcH/HpaI aldolase
KeywordsLYASE / Class II pyruvate aldolase / metal dependent / aldol reaction / Hydroxypyruvate / pyruvate / aldolase / carbon bond formation / holo
Function / homologyHpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / catalytic activity / 3-HYDROXYPYRUVIC ACID / : / HpcH/HpaI aldolase
Function and homology information
Biological speciesSphingomonas wittichii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLaustsen, J. / Justo, I. / Marsden, S.R. / Hanefeld, U. / Bento, I.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Substrate Induced Movement of the Metal Cofactor between Active and Resting State.
Authors: Marsden, S.R. / Wijma, H.J. / Mohr, M.K.F. / Justo, I. / Hagedoorn, P.L. / Laustsen, J. / Jeffries, C.M. / Svergun, D. / Mestrom, L. / McMillan, D.G.G. / Bento, I. / Hanefeld, U.
History
DepositionApr 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 7, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HpcH/HpaI aldolase
B: HpcH/HpaI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8787
Polymers53,6472
Non-polymers2315
Water11,151619
1
A: HpcH/HpaI aldolase
B: HpcH/HpaI aldolase
hetero molecules

A: HpcH/HpaI aldolase
B: HpcH/HpaI aldolase
hetero molecules

A: HpcH/HpaI aldolase
B: HpcH/HpaI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,63421
Polymers160,9416
Non-polymers69315
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area24620 Å2
ΔGint-202 kcal/mol
Surface area45280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.094, 71.094, 222.394
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-686-

HOH

21A-703-

HOH

31A-711-

HOH

41A-713-

HOH

51A-714-

HOH

61B-417-

HOH

71B-601-

HOH

81B-670-

HOH

91B-678-

HOH

101B-682-

HOH

111B-697-

HOH

121B-703-

HOH

131B-704-

HOH

141B-705-

HOH

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Components

#1: Protein HpcH/HpaI aldolase


Mass: 26823.561 Da / Num. of mol.: 2 / Mutation: F210W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273) (bacteria)
Strain: RW1 / DSM 6014 / JCM 10273 / Gene: Swit_5035 / Production host: Escherichia coli (E. coli) / References: UniProt: A5VH82
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-3PY / 3-HYDROXYPYRUVIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 35.82 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES, Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2019
RadiationMonochromator: Oxforf-FNB / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.2→59.34 Å / Num. obs: 131067 / % possible obs: 99.9 % / Redundancy: 9.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.052 / Rrim(I) all: 0.16 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
6.57-59.3410.20.0827960.9960.0270.08799.7
1.2-1.228.61.90364970.5420.6782.026100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
REFMAC5.8.0267refinement
XDSdata reduction
BIOMOLdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R62

6r62


Resolution: 1.2→35.55 Å / SU ML: 0.1067 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 16.148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1571 6617 5.05 %
Rwork0.129 124397 -
obs0.1305 131014 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.41 Å2
Refinement stepCycle: LAST / Resolution: 1.2→35.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 11 619 4392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834008
X-RAY DIFFRACTIONf_angle_d1.11035482
X-RAY DIFFRACTIONf_chiral_restr0.0827620
X-RAY DIFFRACTIONf_plane_restr0.0126736
X-RAY DIFFRACTIONf_dihedral_angle_d6.9339598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.26592410.21334103X-RAY DIFFRACTION99.77
1.21-1.230.24162150.21364245X-RAY DIFFRACTION99.91
1.23-1.240.22232240.20824056X-RAY DIFFRACTION99.63
1.24-1.260.24441940.19894156X-RAY DIFFRACTION99.66
1.26-1.280.22852200.19124162X-RAY DIFFRACTION99.91
1.28-1.290.23582300.19944136X-RAY DIFFRACTION99.7
1.29-1.310.22632470.19054080X-RAY DIFFRACTION99.91
1.31-1.330.19131990.16674187X-RAY DIFFRACTION100
1.33-1.350.19592610.1584103X-RAY DIFFRACTION99.86
1.35-1.370.19972330.15684150X-RAY DIFFRACTION99.95
1.37-1.40.17081920.15244167X-RAY DIFFRACTION100
1.4-1.420.19352320.14484157X-RAY DIFFRACTION100
1.42-1.450.20332130.13944156X-RAY DIFFRACTION99.82
1.45-1.480.17932050.13254157X-RAY DIFFRACTION99.79
1.48-1.510.15692060.13254166X-RAY DIFFRACTION99.91
1.51-1.550.17181920.11384169X-RAY DIFFRACTION99.98
1.55-1.590.15942090.11444146X-RAY DIFFRACTION100
1.59-1.630.15381950.10654178X-RAY DIFFRACTION100
1.63-1.680.14041900.10574156X-RAY DIFFRACTION100
1.68-1.730.15362220.10394208X-RAY DIFFRACTION99.98
1.73-1.790.14422030.10594118X-RAY DIFFRACTION99.98
1.79-1.860.13972030.11064180X-RAY DIFFRACTION99.98
1.86-1.950.13752300.11084117X-RAY DIFFRACTION99.86
1.95-2.050.14172490.11234144X-RAY DIFFRACTION100
2.05-2.180.1332090.11094151X-RAY DIFFRACTION100
2.18-2.350.13932440.11044140X-RAY DIFFRACTION99.98
2.35-2.580.13922360.11674137X-RAY DIFFRACTION99.95
2.59-2.960.14172440.12624108X-RAY DIFFRACTION99.82
2.96-3.730.15462420.1224129X-RAY DIFFRACTION100
3.73-35.550.1352370.13174135X-RAY DIFFRACTION99.82

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