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- PDB-7o5i: Crystal structure of apo-SwHKA (Hydroxy ketone aldolase) from Sph... -

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Basic information

Entry
Database: PDB / ID: 7o5i
TitleCrystal structure of apo-SwHKA (Hydroxy ketone aldolase) from Sphingomonas wittichii RW1
ComponentsHpcH/HpaI aldolase
KeywordsLYASE / Class II pyruvate aldolase / Metal dependent aldolase / aldol reaction / carbon bond formation / apo
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 / BROMIDE ION / : / DI(HYDROXYETHYL)ETHER / HpcH/HpaI aldolase
Function and homology information
Biological speciesSphingomonas wittichii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 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 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 7, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HpcH/HpaI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4407
Polymers26,9231
Non-polymers5176
Water5,963331
1
A: HpcH/HpaI aldolase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)164,64042
Polymers161,5366
Non-polymers3,10436
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation13_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation19_655-x+3/2,-z+1/2,-y+1/21
crystal symmetry operation22_554z+1/2,-y+1/2,x-1/21
Buried area29000 Å2
ΔGint-140 kcal/mol
Surface area45070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.376, 116.376, 116.376
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number208
Space group name H-MP4232
Space group name HallP4n23
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21A-616-

HOH

31A-650-

HOH

41A-675-

HOH

51A-676-

HOH

61A-679-

HOH

71A-687-

HOH

81A-688-

HOH

91A-691-

HOH

101A-703-

HOH

111A-706-

HOH

121A-719-

HOH

131A-725-

HOH

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Components

#1: Protein HpcH/HpaI aldolase


Mass: 26922.670 Da / Num. of mol.: 1
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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O3
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Br
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.15 %
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: Mar 26, 2021
RadiationMonochromator: Oxford-FNB / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.35→116.38 Å / Num. obs: 59487 / % possible obs: 100 % / Redundancy: 20.3 % / Biso Wilson estimate: 16.95 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.025 / Rrim(I) all: 0.114 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allDiffraction-ID
7.39-116.380.06333.24630.0160.0651
1.35-1.372.3191.728920.6272.4051

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→52.04 Å / SU ML: 0.1101 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.8811
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1606 2870 4.85 %
Rwork0.1322 56350 -
obs0.1335 59220 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.92 Å2
Refinement stepCycle: LAST / Resolution: 1.35→52.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 18 331 2242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052027
X-RAY DIFFRACTIONf_angle_d1.09542762
X-RAY DIFFRACTIONf_chiral_restr0.0894312
X-RAY DIFFRACTIONf_plane_restr0.0139370
X-RAY DIFFRACTIONf_dihedral_angle_d9.1309305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.27671240.25192773X-RAY DIFFRACTION99.45
1.37-1.40.24061390.1962782X-RAY DIFFRACTION100
1.4-1.430.14831240.1582756X-RAY DIFFRACTION99.79
1.43-1.450.20391220.15422812X-RAY DIFFRACTION99.66
1.45-1.490.22381380.16512751X-RAY DIFFRACTION99.14
1.49-1.520.16521450.14062780X-RAY DIFFRACTION99.63
1.52-1.560.17091410.12422763X-RAY DIFFRACTION99.62
1.56-1.60.14071720.11532774X-RAY DIFFRACTION99.97
1.6-1.650.14111390.10992778X-RAY DIFFRACTION99.9
1.65-1.70.15361330.11552809X-RAY DIFFRACTION99.93
1.7-1.760.18291320.13462813X-RAY DIFFRACTION99.97
1.76-1.830.17231440.12832814X-RAY DIFFRACTION99.93
1.83-1.920.16791640.12812745X-RAY DIFFRACTION98.74
1.92-2.020.16781520.12372769X-RAY DIFFRACTION98.45
2.02-2.140.15451540.12062816X-RAY DIFFRACTION99.87
2.14-2.310.14121480.11672830X-RAY DIFFRACTION100
2.31-2.540.15251490.11332859X-RAY DIFFRACTION100
2.54-2.910.14831490.12362892X-RAY DIFFRACTION99.93
2.91-3.660.16591510.13362922X-RAY DIFFRACTION99.97
3.67-52.040.15481500.14493112X-RAY DIFFRACTION99.82

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