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- PDB-8adq: Crystal structure of holo-SwHPA-Mg (hydroxy ketone aldolase) from... -

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Basic information

Entry
Database: PDB / ID: 8adq
TitleCrystal structure of holo-SwHPA-Mg (hydroxy ketone aldolase) from Sphingomonas wittichii RW1 in complex with hydroxypyruvate and D-Glyceraldehyde
ComponentsHpcH/HpaI aldolase
KeywordsLYASE / Hydroxy-keto aldolase / aldol condensation / aldol cleavage / stereospecificity / TIM barrel fold
Function / homology
Function and homology information


HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
D-Glyceraldehyde / 3-HYDROXYPYRUVIC ACID / BROMIDE ION / : / DI(HYDROXYETHYL)ETHER / HpcH/HpaI aldolase
Similarity search - Component
Biological speciesRhizorhabdus wittichii RW1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJusto, I. / Marsden, S.R. / Hanefeld, U. / Bento, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionJul 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: HpcH/HpaI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,58614
Polymers27,4681
Non-polymers1,11813
Water4,342241
1
A: HpcH/HpaI aldolase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)171,51784
Polymers164,8106
Non-polymers6,70878
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_555-y+1/2,-x+1/2,-z+1/21
crystal symmetry operation19_555-x+1/2,-z+1/2,-y+1/21
crystal symmetry operation24_555-z+1/2,-y+1/2,-x+1/21
Buried area35700 Å2
ΔGint-126 kcal/mol
Surface area44850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.793, 115.793, 115.793
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number208
Space group name H-MP4232
Space group name HallP4n23
Symmetry operation#1: x,y,z
#2: x+1/2,-z+1/2,y+1/2
#3: x+1/2,z+1/2,-y+1/2
#4: z+1/2,y+1/2,-x+1/2
#5: -z+1/2,y+1/2,x+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y+1/2,x+1/2,-z+1/2
#20: -y+1/2,-x+1/2,-z+1/2
#21: z+1/2,-y+1/2,x+1/2
#22: -z+1/2,-y+1/2,-x+1/2
#23: -x+1/2,z+1/2,y+1/2
#24: -x+1/2,-z+1/2,-y+1/2
Components on special symmetry positions
IDModelComponents
11A-582-

HOH

21A-587-

HOH

31A-595-

HOH

41A-616-

HOH

51A-617-

HOH

61A-622-

HOH

71A-625-

HOH

81A-629-

HOH

91A-631-

HOH

101A-633-

HOH

111A-637-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein HpcH/HpaI aldolase


Mass: 27468.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizorhabdus wittichii RW1 (bacteria)
Strain: DSM 6014 / CCUG 31198 / JCM 15750 / NBRC 105917 / EY 4224 / RW1
Gene: Swit_5035 / Production host: Escherichia coli (E. coli) / References: UniProt: A5VH82
#3: Sugar ChemComp-3GR / D-Glyceraldehyde / GLYCERALDEHYDE / (2R)-2,3-DIHYDROXYPROPANAL


Type: D-saccharide / Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 6 types, 252 molecules

#2: 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
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#7: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.44 M-0.65 M sodium citrate 0.1 M HEPES at pH 7.0.

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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: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2021
RadiationMonochromator: MD2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.6→40.9 Å / Num. obs: 35573 / % possible obs: 99.96 % / Redundancy: 38.5 % / Biso Wilson estimate: 29.67 Å2 / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.0116 / Rrim(I) all: 0.0721 / Rsym value: 0.071 / Net I/σ(I): 30.94
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 39.9 % / Rmerge(I) obs: 2.98 / Mean I/σ(I) obs: 1.26 / Num. unique obs: 3490 / CC1/2: 0.65 / CC star: 0.89 / Rpim(I) all: 0.48 / Rrim(I) all: 3.02 / % possible all: 99.91

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Processing

Software
NameVersionClassification
REFMAC1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6r62

6r62


Resolution: 1.6→40.9 Å / SU ML: 0.2008 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2293
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 1766 4.97 %5%
Rwork0.1679 33802 --
obs0.1695 35568 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.29 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 47 241 2171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111979
X-RAY DIFFRACTIONf_angle_d1.16372678
X-RAY DIFFRACTIONf_chiral_restr0.0638303
X-RAY DIFFRACTIONf_plane_restr0.0139356
X-RAY DIFFRACTIONf_dihedral_angle_d12.5505293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.32191410.28182534X-RAY DIFFRACTION99.89
1.64-1.690.3361410.27442535X-RAY DIFFRACTION99.96
1.69-1.750.33881220.28692564X-RAY DIFFRACTION100
1.75-1.810.2671210.23972565X-RAY DIFFRACTION100
1.81-1.880.26631290.21282564X-RAY DIFFRACTION99.96
1.88-1.970.23191390.18842553X-RAY DIFFRACTION100
1.97-2.070.19911440.1842571X-RAY DIFFRACTION99.96
2.07-2.20.21511210.17932587X-RAY DIFFRACTION100
2.2-2.370.20861390.16212588X-RAY DIFFRACTION100
2.37-2.610.19891510.15842586X-RAY DIFFRACTION100
2.61-2.990.22241320.17892642X-RAY DIFFRACTION100
2.99-3.760.18951540.15472650X-RAY DIFFRACTION100
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)
13.492521658060.532399512729-1.196042756543.508792649370.2365038593812.844629646810.0721742815487-0.7242359476440.04855128413570.468776201817-0.1409379462470.3661611857510.0119182177453-0.03127533930180.07566842300020.280927249206-0.0579842420909-0.04498544018010.424290248927-0.05188698945290.350260996079-1.9993811477128.467684185936.1894035216
20.6369404205320.1531090930280.3111506656921.36062751122-0.1382623604890.990199232110.0278980421848-0.1096168161880.0726872143558-0.0921049228268-0.01578100272430.1434767500430.0539455332933-0.127210999998-0.01633437132570.279708261079-0.069813195298-0.05519768107180.342010970105-0.04969354977710.3114144080035.2421359413523.861391469126.1152934628
31.579635914261.260600647750.3795089720831.645503139210.2752577605411.08775215366-0.0664289969918-0.1274825503210.327773715353-0.101857446855-0.05349998904360.417810160807-0.0918591260881-0.2308419041670.120529066240.293190546667-0.0169272775249-0.1079466732630.327910152279-0.06897817021570.420380996526-1.6127840485439.740050048922.9425965361
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 19 )0 - 191 - 20
22chain 'A' and (resid 20 through 186 )20 - 18621 - 187
33chain 'A' and (resid 187 through 251 )187 - 251188 - 252

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