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- PDB-7nr1: Crystal structure of holo-S116A mutant of Hydroxy ketone aldolase... -

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Basic information

Entry
Database: PDB / ID: 7nr1
TitleCrystal structure of holo-S116A 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
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 / HpcH/HpaI aldolase
Function and homology information
Biological speciesSphingomonas wittichii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionMar 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 7, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Jan 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
A: HpcH/HpaI aldolase
B: HpcH/HpaI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2853
Polymers53,2612
Non-polymers241
Water1,13563
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)159,8559
Polymers159,7826
Non-polymers733
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 area22640 Å2
ΔGint-201 kcal/mol
Surface area45150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.052, 71.052, 222.689
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-420-

HOH

21A-425-

HOH

31A-435-

HOH

41A-436-

HOH

51A-437-

HOH

61A-438-

HOH

71A-439-

HOH

81B-322-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 251 / Label seq-ID: 1 - 251

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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

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Components

#1: Protein HpcH/HpaI aldolase


Mass: 26630.377 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.03 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 400, 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: 2.3→74.23 Å / Num. obs: 18614 / % possible obs: 100 % / Redundancy: 8.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.102 / Rrim(I) all: 0.215 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
8.91-74.239.80.0573260.9990.0280.06499.8
2.3-2.386.11.41817920.4080.9341.70699.9

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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: 2.3→59.31 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.882 / SU ML: 0.246 / Cross valid method: FREE R-VALUE / ESU R: 0.627 / ESU R Free: 0.273
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2512 910 4.894 %
Rwork0.2149 17684 -
all0.217 --
obs-18594 99.882 %
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: 39.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.303 Å2-0.151 Å2-0 Å2
2---0.303 Å2-0 Å2
3---0.982 Å2
Refinement stepCycle: LAST / Resolution: 2.3→59.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 1 63 3808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133822
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173672
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.6325192
X-RAY DIFFRACTIONr_angle_other_deg1.1091.5738408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.415500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.71720.816196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55415588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1831534
X-RAY DIFFRACTIONr_chiral_restr0.0590.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024412
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02864
X-RAY DIFFRACTIONr_nbd_refined0.1440.2629
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1260.23317
X-RAY DIFFRACTIONr_nbtor_refined0.1250.21812
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.21816
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0880.297
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0720.212
X-RAY DIFFRACTIONr_nbd_other0.1210.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0690.212
X-RAY DIFFRACTIONr_mcbond_it1.4854.12006
X-RAY DIFFRACTIONr_mcbond_other1.4854.12005
X-RAY DIFFRACTIONr_mcangle_it2.3836.1472504
X-RAY DIFFRACTIONr_mcangle_other2.3826.1482505
X-RAY DIFFRACTIONr_scbond_it1.5584.3161816
X-RAY DIFFRACTIONr_scbond_other1.5424.3181812
X-RAY DIFFRACTIONr_scangle_it2.626.3922688
X-RAY DIFFRACTIONr_scangle_other2.6186.3932688
X-RAY DIFFRACTIONr_lrange_it4.05948.4783899
X-RAY DIFFRACTIONr_lrange_other4.05848.4863898
X-RAY DIFFRACTIONr_ncsr_local_group_10.0690.057667
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.069270.05009
12BX-RAY DIFFRACTIONLocal ncs0.069270.05009
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
2.3-2.360.338550.32713110.32813680.6730.69599.85380.324
2.36-2.4240.318670.31712480.31713150.7580.7311000.312
2.424-2.4940.352750.28412430.28813190.7610.78299.92420.277
2.494-2.5710.27780.27411950.27312730.8260.8181000.266
2.571-2.6550.309640.26411570.26612220.8230.85599.91820.25
2.655-2.7480.281870.2311020.23311890.8680.8971000.215
2.748-2.8520.282470.23311090.23511560.8620.8971000.213
2.852-2.9680.329470.23510500.23910970.8560.8951000.212
2.968-3.0990.259440.22810140.22910580.8810.8911000.206
3.099-3.250.29440.2089660.21210110.8950.90899.90110.19
3.25-3.4260.218430.1969190.1979620.9190.9361000.179
3.426-3.6330.205400.1788530.1798960.9410.94299.66520.167
3.633-3.8820.286370.1938290.1968670.9030.93499.88470.181
3.882-4.1920.205320.1737680.1748010.9540.95299.87520.163
4.192-4.590.175330.1796860.1787220.9620.95699.58450.171
4.59-5.1280.232390.186240.1836660.9420.95699.54960.177
5.128-5.9130.382130.25810.2045960.910.9499.66440.194
5.913-7.2250.225330.2014620.2034970.9310.94199.59760.195
7.225-10.1420.17230.23580.1993820.970.96599.73820.196
10.142-59.310.15490.2392090.2362180.9720.9621000.238

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