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- PDB-7o5w: Crystal structure of holo-F210W mutant of Hydroxy ketone aldolase... -

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Basic information

Entry
Database: PDB / ID: 7o5w
TitleCrystal structure of holo-F210W mutant of Hydroxy ketone aldolase (SwHKA)from Sphingomonas wittichii RW1
ComponentsHpcH/HpaI aldolase
KeywordsLYASE / Class II pyruvate aldolase / Metal dependent aldolase / aldol reaction / Magnesium / carbon bond formation / holo / mutant
Function / homologyHpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase family / 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: 1.2 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 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 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)54,54414
Polymers53,6472
Non-polymers89712
Water10,899605
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


  • defined by author&software
  • Evidence: gel filtration
  • 164 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)163,63342
Polymers160,9416
Non-polymers2,69136
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 area28070 Å2
ΔGint-202 kcal/mol
Surface area44910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.996, 70.996, 222.817
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
11AAA-417-

HOH

21AAA-621-

HOH

31AAA-674-

HOH

41AAA-683-

HOH

51AAA-706-

HOH

61AAA-710-

HOH

71BBB-443-

HOH

81BBB-663-

HOH

91BBB-668-

HOH

101BBB-680-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 1 - 249 / Label seq-ID: 2 - 250

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein HpcH/HpaI aldolase


Mass: 26823.561 Da / Num. of mol.: 2 / Mutation: F210W
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, 617 molecules

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


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


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 1.91 Å3/Da / Density % sol: 35.76 %
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: 0.9762 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: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.2→74.27 Å / Num. obs: 130983 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.039 / Rrim(I) all: 0.087 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
6.57-74.2710.60.0537980.9970.0260.059
1.2-1.229.50.47864380.9060.2470.539

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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: 1.2→53.889 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.999 / SU ML: 0.021 / Cross valid method: FREE R-VALUE / ESU R: 0.033 / ESU R Free: 0.034
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1463 6604 5.042 %
Rwork0.1185 124376 -
all0.12 --
obs-130980 99.987 %
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: 11.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.091 Å2-0.046 Å20 Å2
2---0.091 Å2-0 Å2
3---0.296 Å2
Refinement stepCycle: LAST / Resolution: 1.2→53.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3753 0 30 605 4388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0133917
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173740
X-RAY DIFFRACTIONr_angle_refined_deg2.0191.6315300
X-RAY DIFFRACTIONr_angle_other_deg1.6691.5728586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9155518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.32820.75200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69115605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0521535
X-RAY DIFFRACTIONr_chiral_restr0.1270.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02882
X-RAY DIFFRACTIONr_nbd_refined0.2270.2863
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.23721
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21958
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21992
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.2327
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.4730.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3070.234
X-RAY DIFFRACTIONr_nbd_other0.2620.2110
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2650.259
X-RAY DIFFRACTIONr_mcbond_it1.1220.9812024
X-RAY DIFFRACTIONr_mcbond_other1.120.982023
X-RAY DIFFRACTIONr_mcangle_it1.321.4812531
X-RAY DIFFRACTIONr_mcangle_other1.3211.4812532
X-RAY DIFFRACTIONr_scbond_it2.1521.2511893
X-RAY DIFFRACTIONr_scbond_other2.1321.2511883
X-RAY DIFFRACTIONr_scangle_it2.3981.7872760
X-RAY DIFFRACTIONr_scangle_other2.3981.7882761
X-RAY DIFFRACTIONr_lrange_it2.49314.0164523
X-RAY DIFFRACTIONr_lrange_other2.1213.1464361
X-RAY DIFFRACTIONr_rigid_bond_restr4.07537653
X-RAY DIFFRACTIONr_ncsr_local_group_10.0910.057847
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.09120.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.09120.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.1784900.1469182X-RAY DIFFRACTION100
1.231-1.2650.1634600.1349008X-RAY DIFFRACTION100
1.265-1.3020.184800.1228699X-RAY DIFFRACTION99.9782
1.302-1.3420.1414840.1088452X-RAY DIFFRACTION100
1.342-1.3860.1554360.1048165X-RAY DIFFRACTION100
1.386-1.4340.1354020.17968X-RAY DIFFRACTION100
1.434-1.4880.1414200.0967697X-RAY DIFFRACTION99.9877
1.488-1.5490.1263310.0887428X-RAY DIFFRACTION99.9742
1.549-1.6180.1453290.097080X-RAY DIFFRACTION100
1.618-1.6970.1333520.0946790X-RAY DIFFRACTION100
1.697-1.7890.1453090.16411X-RAY DIFFRACTION99.9702
1.789-1.8970.1333200.1026125X-RAY DIFFRACTION100
1.897-2.0280.133290.1065697X-RAY DIFFRACTION100
2.028-2.190.1432780.1155291X-RAY DIFFRACTION100
2.19-2.3990.1492970.124858X-RAY DIFFRACTION99.9612
2.399-2.6820.152410.1324422X-RAY DIFFRACTION99.9357
2.682-3.0960.1622370.1393888X-RAY DIFFRACTION100
3.096-3.790.1421770.1323262X-RAY DIFFRACTION100
3.79-5.3530.141550.1292542X-RAY DIFFRACTION99.8889

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