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- PDB-7o5r: Crystal structure of holo-SwHPA-Mn (hydroxyketoacid aldolase) fro... -

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Basic information

Entry
Database: PDB / ID: 7o5r
TitleCrystal structure of holo-SwHPA-Mn (hydroxyketoacid aldolase) from Sphingomonas wittichii RW1
Componentshydroxyketoacid aldolase
KeywordsLYASE / Class II Pyruvate Aldolase / Metal Dependent / Aldol Reaction / Aldolase / holo / Manganese / Carbon Bond Formation
Function / homologyBROMIDE ION / : / :
Function and homology information
Biological speciesRhizorhabdus wittichii RW1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLaustsen, J. / Justo, 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
DepositionApr 9, 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 1.3May 1, 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: hydroxyketoacid aldolase
B: hydroxyketoacid aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9319
Polymers53,5692
Non-polymers3627
Water8,359464
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-43 kcal/mol
Surface area19570 Å2
Unit cell
Length a, b, c (Å)71.540, 71.540, 225.394
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
11B-303-

K

21A-416-

HOH

31A-423-

HOH

41A-448-

HOH

51A-599-

HOH

61A-612-

HOH

71A-615-

HOH

81A-617-

HOH

91A-621-

HOH

101A-623-

HOH

111A-626-

HOH

121A-627-

HOH

131A-628-

HOH

141A-629-

HOH

151A-630-

HOH

161B-607-

HOH

171B-628-

HOH

181B-630-

HOH

191B-634-

HOH

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Components

#1: Protein hydroxyketoacid aldolase


Mass: 26784.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizorhabdus wittichii RW1 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
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: Dec 10, 2018
RadiationMonochromator: Oxforf-FNB / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.7562
pseudo-merohedral22K, H, -L20.2438
ReflectionResolution: 1.65→75.131 Å / Num. obs: 51766 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.106 / Rrim(I) all: 0.184 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
9.04-75.136.20.0593220.9960.0390.07199.2
1.65-1.6860.99726000.3250.691.222100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo-SwHKA

Resolution: 1.65→75.131 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.177 / WRfactor Rwork: 0.147 / SU B: 1.366 / SU ML: 0.05 / Average fsc free: 0.9776 / Average fsc work: 0.9865 / Cross valid method: FREE R-VALUE / ESU R: 0.021 / ESU R Free: 0.02
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1931 2506 4.841 %
Rwork0.1596 49255 -
all0.161 --
obs-51761 99.929 %
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: 11.952 Å2
Baniso -1Baniso -2Baniso -3
1--0.316 Å2-0 Å2-0 Å2
2---0.316 Å2-0 Å2
3---0.633 Å2
Refinement stepCycle: LAST / Resolution: 1.65→75.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3754 0 7 464 4225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123918
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163629
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.6375328
X-RAY DIFFRACTIONr_angle_other_deg0.6311.5588422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.267535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62910607
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.42310166
X-RAY DIFFRACTIONr_chiral_restr0.0930.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02770
X-RAY DIFFRACTIONr_nbd_refined0.2380.2878
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.23425
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21947
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22146
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2328
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1540.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1950.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.340.233
X-RAY DIFFRACTIONr_nbd_other0.1630.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2270.268
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2540.212
X-RAY DIFFRACTIONr_mcbond_it1.3281.1972048
X-RAY DIFFRACTIONr_mcbond_other1.321.1962048
X-RAY DIFFRACTIONr_mcangle_it1.9161.7922567
X-RAY DIFFRACTIONr_mcangle_other1.9181.7932568
X-RAY DIFFRACTIONr_scbond_it1.9061.4061870
X-RAY DIFFRACTIONr_scbond_other1.8761.4071862
X-RAY DIFFRACTIONr_scangle_it2.7892.0332754
X-RAY DIFFRACTIONr_scangle_other2.7882.0332755
X-RAY DIFFRACTIONr_lrange_it4.76320.7124590
X-RAY DIFFRACTIONr_lrange_other4.51119.324442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.2641760.2013682X-RAY DIFFRACTION99.8706
1.693-1.7390.2421820.1793542X-RAY DIFFRACTION100
1.739-1.790.2841800.1963470X-RAY DIFFRACTION99.9179
1.79-1.8450.2761750.213299X-RAY DIFFRACTION99.8563
1.845-1.9050.2231560.1993276X-RAY DIFFRACTION100
1.905-1.9720.2381670.1793141X-RAY DIFFRACTION100
1.972-2.0460.221560.1763043X-RAY DIFFRACTION100
2.046-2.130.21440.162907X-RAY DIFFRACTION100
2.13-2.2240.1841240.152824X-RAY DIFFRACTION100
2.224-2.3330.2061390.1642663X-RAY DIFFRACTION99.9287
2.333-2.4590.1811190.1572577X-RAY DIFFRACTION100
2.459-2.6080.1991450.1572366X-RAY DIFFRACTION100
2.608-2.7880.1651110.1462273X-RAY DIFFRACTION99.9581
2.788-3.0110.191090.1552101X-RAY DIFFRACTION99.7292
3.011-3.2980.1641010.1461924X-RAY DIFFRACTION100
3.298-3.6860.179860.1411756X-RAY DIFFRACTION99.8374
3.686-4.2550.151750.1221548X-RAY DIFFRACTION100
4.255-5.2070.123800.1311290X-RAY DIFFRACTION99.8542
5.207-7.3460.136490.1811012X-RAY DIFFRACTION99.3446
7.346-75.1310.213320.16561X-RAY DIFFRACTION99.4966

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