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- PDB-7nnk: Crystal structure of S116A mutant of hydroxy ketone aldolase (SwH... -

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Basic information

Entry
Database: PDB / ID: 7nnk
TitleCrystal structure of S116A mutant of hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1 in complex with hydroxypyruvate
ComponentsHpcH/HpaI aldolase
KeywordsLYASE / Class II Pyruvate Aldolase / Metal Dependent / Aldol Reaction / Hydroxypyruvate / Pyruvate / Aldolase / Class II
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: 1.8 Å
AuthorsJusto, 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
DepositionFeb 25, 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 1.3Jan 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,6905
Polymers53,5372
Non-polymers1533
Water5,386299
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)161,06915
Polymers160,6116
Non-polymers4589
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area23280 Å2
ΔGint-209 kcal/mol
Surface area44640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.327, 71.327, 223.185
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-454-

HOH

31A-534-

HOH

41A-559-

HOH

51A-562-

HOH

61A-563-

HOH

71A-564-

HOH

81B-403-

HOH

91B-533-

HOH

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Components

#1: Protein HpcH/HpaI aldolase / Hydroxy Ketoacid Aldolase


Mass: 26768.525 Da / Num. of mol.: 2 / Mutation: S116A
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-3PY / 3-HYDROXYPYRUVIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG400, HEPES, Magnesium Chloride

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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: Nov 17, 2020
RadiationMonochromator: Oxford-FNB / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→74.39 Å / Num. obs: 38705 / % possible obs: 98.5 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.085 / Rrim(I) all: 0.132 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
9-74.393.60.0262970.9990.0220.03592.8
1.8-1.843.21.19622920.3651.0371.58999

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Processing

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

6r62


Resolution: 1.8→59.533 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.171 / SU B: 3.708 / SU ML: 0.111 / Average fsc free: 0.8879 / Average fsc work: 0.9052 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2247 1936 5.002 %
Rwork0.1831 36765 -
all0.185 --
obs-38701 98.533 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.099 Å2
Baniso -1Baniso -2Baniso -3
1--0.165 Å2-0.083 Å20 Å2
2---0.165 Å20 Å2
3---0.536 Å2
Refinement stepCycle: LAST / Resolution: 1.8→59.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3731 0 9 299 4039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133886
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173700
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.6335282
X-RAY DIFFRACTIONr_angle_other_deg1.3431.5748488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9545517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.64421.005199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60815592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4541533
X-RAY DIFFRACTIONr_chiral_restr0.0870.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024508
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02874
X-RAY DIFFRACTIONr_nbd_refined0.1840.2702
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1460.23353
X-RAY DIFFRACTIONr_nbtor_refined0.1420.21842
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21789
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2235
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1160.225
X-RAY DIFFRACTIONr_nbd_other0.1220.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.244
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0020.21
X-RAY DIFFRACTIONr_mcbond_it1.5292.2162038
X-RAY DIFFRACTIONr_mcbond_other1.5252.2172036
X-RAY DIFFRACTIONr_mcangle_it2.1133.3172553
X-RAY DIFFRACTIONr_mcangle_other2.1123.3172554
X-RAY DIFFRACTIONr_scbond_it2.0832.441848
X-RAY DIFFRACTIONr_scbond_other2.0742.441843
X-RAY DIFFRACTIONr_scangle_it3.1393.5752725
X-RAY DIFFRACTIONr_scangle_other3.1383.5742726
X-RAY DIFFRACTIONr_lrange_it4.35126.9594141
X-RAY DIFFRACTIONr_lrange_other4.18526.6684079
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.3151750.28927060.2929070.7250.7399.10560.285
1.847-1.8970.2951470.25726440.25928200.7940.82698.97160.25
1.897-1.9520.2741120.23126030.23327420.8420.86999.01530.219
1.952-2.0120.2991340.22325080.22726730.8550.87298.84030.204
2.012-2.0780.2291130.19524560.19726040.9040.90798.65590.176
2.078-2.1510.246890.1923850.19224960.9090.91799.11860.169
2.151-2.2320.242930.17923460.18124560.9090.92699.30780.158
2.232-2.3230.2191340.17621210.17822860.9270.93798.64390.154
2.323-2.4260.231340.16220960.16622470.930.94899.24340.144
2.426-2.5440.1861150.15419810.15621330.9460.95298.26540.138
2.544-2.6820.2191050.16519100.16820360.9350.94998.96860.148
2.682-2.8440.24660.1618260.16219180.9340.95598.64440.145
2.844-3.040.185850.16616850.16717890.9440.95398.9380.155
3.04-3.2830.1961020.17715480.17816870.9340.94497.80680.166
3.283-3.5950.227820.17614180.17915510.9280.94196.71180.171
3.595-4.0180.25720.1712750.17413920.8810.93696.76720.169
4.018-4.6360.206610.1711460.17212280.9260.94198.28990.171
4.636-5.6690.192550.1739690.17410470.9480.95297.80320.176
5.669-7.9810.232380.2017340.2028060.9080.92995.78160.204
7.981-59.5330.173240.24070.1994570.9710.95494.31070.205

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