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- PDB-7o9r: Crystal structure of holo-H44A mutant of Hydroxy ketone aldolase ... -

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Basic information

Entry
Database: PDB / ID: 7o9r
TitleCrystal structure of holo-H44A mutant of Hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1
ComponentsHpcH/HpaI aldolase
KeywordsLYASE / Class II Pyruvate Aldolase / Metal dependent / Aldol reaction / Magnesium / 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 / BROMIDE ION / : / DI(HYDROXYETHYL)ETHER / HpcH/HpaI aldolase
Function and homology information
Biological speciesSphingomonas wittichii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 16, 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

Downloads & links

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Assembly

Deposited unit
AAA: HpcH/HpaI aldolase
BBB: HpcH/HpaI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,18614
Polymers53,4352
Non-polymers75112
Water3,891216
1
AAA: HpcH/HpaI aldolase
BBB: HpcH/HpaI aldolase
hetero molecules

AAA: HpcH/HpaI aldolase
BBB: HpcH/HpaI aldolase
hetero molecules

AAA: HpcH/HpaI aldolase
BBB: HpcH/HpaI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,55942
Polymers160,3056
Non-polymers2,25436
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.881, 70.881, 223.180
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
11BBB-304-

K

21AAA-504-

HOH

31AAA-517-

HOH

41AAA-520-

HOH

51AAA-521-

HOH

61AAA-522-

HOH

71BBB-491-

HOH

81BBB-493-

HOH

91BBB-494-

HOH

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein HpcH/HpaI aldolase


Mass: 26717.455 Da / Num. of mol.: 2 / Mutation: H44A
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

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Non-polymers , 5 types, 228 molecules

#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.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.03 Å3/Da / Density % sol: 39.42 %
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: Apr 26, 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: 1.85→59.19 Å / Num. obs: 33572 / % possible obs: 94 % / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.094 / Rrim(I) all: 0.18 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.06-59.194.60.0592720.9980.0350.069
1.85-1.893.71.53721590.6020.9161.801

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R62

6r62


Resolution: 1.85→59.19 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.784 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.154 / ESU R Free: 0.134
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1959 1714 5.133 %
Rwork0.158 31679 -
all0.16 --
obs-33393 93.417 %
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: 27.832 Å2
Baniso -1Baniso -2Baniso -3
1-0.054 Å20.027 Å2-0 Å2
2--0.054 Å20 Å2
3----0.177 Å2
Refinement stepCycle: LAST / Resolution: 1.85→59.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3736 0 15 216 3967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133876
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173734
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.6325270
X-RAY DIFFRACTIONr_angle_other_deg1.3421.5738562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6145517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.69520.65200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89515603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.751536
X-RAY DIFFRACTIONr_chiral_restr0.0670.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02892
X-RAY DIFFRACTIONr_nbd_refined0.2140.2809
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.23589
X-RAY DIFFRACTIONr_nbtor_refined0.1550.21907
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21821
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2178
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0270.21
X-RAY DIFFRACTIONr_metal_ion_refined0.230.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3220.221
X-RAY DIFFRACTIONr_nbd_other0.1960.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.224
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4050.24
X-RAY DIFFRACTIONr_mcbond_it1.8852.7652029
X-RAY DIFFRACTIONr_mcbond_other1.8842.7642028
X-RAY DIFFRACTIONr_mcangle_it2.6874.1392538
X-RAY DIFFRACTIONr_mcangle_other2.6864.142539
X-RAY DIFFRACTIONr_scbond_it2.563.1431847
X-RAY DIFFRACTIONr_scbond_other2.563.1421846
X-RAY DIFFRACTIONr_scangle_it3.8764.5732725
X-RAY DIFFRACTIONr_scangle_other3.8754.5732726
X-RAY DIFFRACTIONr_lrange_it5.3134.3684266
X-RAY DIFFRACTIONr_lrange_other5.25334.244231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.2791240.2222427X-RAY DIFFRACTION95.7942
1.898-1.950.2151270.2012322X-RAY DIFFRACTION95.9264
1.95-2.0060.2471110.1862282X-RAY DIFFRACTION95.9888
2.006-2.0680.2061170.1792241X-RAY DIFFRACTION96.2842
2.068-2.1360.221140.172126X-RAY DIFFRACTION95.8904
2.136-2.2110.186920.1642070X-RAY DIFFRACTION93.8368
2.211-2.2940.239750.1681873X-RAY DIFFRACTION87.5506
2.294-2.3880.187900.1681839X-RAY DIFFRACTION92.0764
2.388-2.4940.251000.1541831X-RAY DIFFRACTION95.311
2.494-2.6150.2091120.1621732X-RAY DIFFRACTION95.0515
2.615-2.7570.2331020.1681672X-RAY DIFFRACTION95.0187
2.757-2.9240.238840.1751563X-RAY DIFFRACTION94.7641
2.924-3.1250.242690.1711420X-RAY DIFFRACTION91.2377
3.125-3.3750.234760.1681227X-RAY DIFFRACTION85.2191
3.375-3.6970.171750.1441217X-RAY DIFFRACTION92.4177
3.697-4.1320.165630.1331113X-RAY DIFFRACTION93.2593
4.132-4.7680.119500.118997X-RAY DIFFRACTION92.6549
4.768-5.8340.208620.143794X-RAY DIFFRACTION90.4863
5.834-8.2250.141460.144596X-RAY DIFFRACTION87.3469

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