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- PDB-7nuj: Crystal structure of holo-SwHPA-Mg (hydroxy ketone aldolase) from... -

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Basic information

Entry
Database: PDB / ID: 7nuj
TitleCrystal structure of holo-SwHPA-Mg (hydroxy ketone aldolase) 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 RW1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionMar 12, 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)53,6184
Polymers53,5692
Non-polymers492
Water7,332407
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)160,85312
Polymers160,7076
Non-polymers1466
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 area22830 Å2
ΔGint-218 kcal/mol
Surface area45680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.102, 71.102, 223.196
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-436-

HOH

21A-441-

HOH

31A-535-

HOH

41A-602-

HOH

51A-604-

HOH

61A-613-

HOH

71A-614-

HOH

81B-587-

HOH

91B-588-

HOH

101B-590-

HOH

111B-592-

HOH

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

NCS domain segments:

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-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

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

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Components

#1: Protein HpcH/HpaI aldolase


Mass: 26784.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas wittichii RW1 (bacteria) / 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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 1.87 Å3/Da / Density % sol: 34.23 %
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: P14 (MX2) / Wavelength: 0.9766 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2019
RadiationMonochromator: Oxford-FMB / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 1.9→59.36 Å / Num. obs: 33131 / % possible obs: 99.9 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.08 / Rrim(I) all: 0.135 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.3 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.11-59.360.0283020.9990.0210.035
1.9-1.941.13721220.5620.8231.413

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Processing

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

6r62


Resolution: 1.9→59.359 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.146 / SU B: 4.348 / SU ML: 0.119 / Average fsc free: 0.8978 / Average fsc work: 0.9051 / Cross valid method: FREE R-VALUE / ESU R: 0.171 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2044 1574 4.751 %
Rwork0.1648 31556 -
all0.167 --
obs-33130 99.876 %
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: 25.889 Å2
Baniso -1Baniso -2Baniso -3
1--1.021 Å2-0.51 Å20 Å2
2---1.021 Å20 Å2
3---3.312 Å2
Refinement stepCycle: LAST / Resolution: 1.9→59.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 0 2 407 4156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133909
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173742
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.6335311
X-RAY DIFFRACTIONr_angle_other_deg1.3091.5758575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6315517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.06820.529208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75415606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3631538
X-RAY DIFFRACTIONr_chiral_restr0.0820.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024533
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02899
X-RAY DIFFRACTIONr_nbd_refined0.1940.2701
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1450.23413
X-RAY DIFFRACTIONr_nbtor_refined0.1380.21891
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.21786
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2310
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.221
X-RAY DIFFRACTIONr_nbd_other0.1230.2110
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.243
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0180.21
X-RAY DIFFRACTIONr_mcbond_it1.6652.5522041
X-RAY DIFFRACTIONr_mcbond_other1.6642.5512040
X-RAY DIFFRACTIONr_mcangle_it2.323.8252555
X-RAY DIFFRACTIONr_mcangle_other2.3193.8252556
X-RAY DIFFRACTIONr_scbond_it2.52.8541868
X-RAY DIFFRACTIONr_scbond_other2.4962.8541865
X-RAY DIFFRACTIONr_scangle_it3.7954.1712752
X-RAY DIFFRACTIONr_scangle_other3.7954.1712752
X-RAY DIFFRACTIONr_lrange_it5.07531.5614272
X-RAY DIFFRACTIONr_lrange_other4.92831.0164166
X-RAY DIFFRACTIONr_ncsr_local_group_10.0650.057820
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.065270.05007
12BX-RAY DIFFRACTIONLocal ncs0.065270.05007
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
1.9-1.950.2831040.30823350.30724410.7480.7299.91810.289
1.95-2.0030.2631320.27122610.2723970.7960.78899.83310.249
2.003-2.0610.2491300.24722020.24723330.8240.81899.95710.227
2.061-2.1240.2461070.21721490.21822570.8510.8799.95570.194
2.124-2.1940.2591060.20820670.21121800.8890.89299.67890.181
2.194-2.2710.2241070.1820080.18221160.9040.91899.95270.154
2.271-2.3560.211860.15819650.1620510.9260.9381000.136
2.356-2.4520.21840.14518830.14819670.9290.951000.121
2.452-2.5610.222840.14117930.14518770.9370.9561000.122
2.561-2.6860.201700.15117280.15317980.9460.9551000.129
2.686-2.8310.183770.14116360.14217150.9570.96299.88340.122
2.831-3.0020.198730.14615450.14916200.9540.95899.87650.127
3.002-3.2090.194800.15114350.15315190.9510.95399.73670.134
3.209-3.4650.169910.12513270.12814190.9620.97199.92950.115
3.465-3.7950.155520.12712290.12812810.9650.9721000.12
3.795-4.240.142500.12911720.12912220.9670.9721000.124
4.24-4.8920.164440.1299750.13110230.970.97599.6090.127
4.892-5.9820.187480.1578360.1598870.9530.95899.66180.155
5.982-8.4170.262330.1946430.1976780.8910.93699.7050.19
8.417-59.3590.283160.2263660.2293880.9470.9498.45360.227

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