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- PDB-6u57: KDO8PS Structure Determined at the EuXFEL using Segmented Flow In... -

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Basic information

Entry
Database: PDB / ID: 6u57
TitleKDO8PS Structure Determined at the EuXFEL using Segmented Flow Injection
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsTRANSFERASE / Catalytic Activity / Transferase Activity
Function / homology
Function and homology information


3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / protein-containing complex / identical protein binding / cytoplasm / cytosol
Similarity search - Function
3-deoxy-8-phosphooctulonate synthase / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase-type TIM barrel
Similarity search - Domain/homology
2-dehydro-3-deoxyphosphooctonate aldolase / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBotha, S. / Ros, A.
Funding support United States, Germany, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM095583 United States
German Research Foundation (DFG)390715994 Germany
CitationJournal: Nat Commun / Year: 2020
Title: Segmented flow generator for serial crystallography at the European X-ray free electron laser.
Authors: Echelmeier, A. / Cruz Villarreal, J. / Messerschmidt, M. / Kim, D. / Coe, J.D. / Thifault, D. / Botha, S. / Egatz-Gomez, A. / Gandhi, S. / Brehm, G. / Conrad, C.E. / Hansen, D.T. / Madsen, C. ...Authors: Echelmeier, A. / Cruz Villarreal, J. / Messerschmidt, M. / Kim, D. / Coe, J.D. / Thifault, D. / Botha, S. / Egatz-Gomez, A. / Gandhi, S. / Brehm, G. / Conrad, C.E. / Hansen, D.T. / Madsen, C. / Bajt, S. / Meza-Aguilar, J.D. / Oberthur, D. / Wiedorn, M.O. / Fleckenstein, H. / Mendez, D. / Knoska, J. / Martin-Garcia, J.M. / Hu, H. / Lisova, S. / Allahgholi, A. / Gevorkov, Y. / Ayyer, K. / Aplin, S. / Ginn, H.M. / Graafsma, H. / Morgan, A.J. / Greiffenberg, D. / Klujev, A. / Laurus, T. / Poehlsen, J. / Trunk, U. / Mezza, D. / Schmidt, B. / Kuhn, M. / Fromme, R. / Sztuk-Dambietz, J. / Raab, N. / Hauf, S. / Silenzi, A. / Michelat, T. / Xu, C. / Danilevski, C. / Parenti, A. / Mekinda, L. / Weinhausen, B. / Mills, G. / Vagovic, P. / Kim, Y. / Kirkwood, H. / Bean, R. / Bielecki, J. / Stern, S. / Giewekemeyer, K. / Round, A.R. / Schulz, J. / Dorner, K. / Grant, T.D. / Mariani, V. / Barty, A. / Mancuso, A.P. / Weierstall, U. / Spence, J.C.H. / Chapman, H.N. / Zatsepin, N. / Fromme, P. / Kirian, R.A. / Ros, A.
History
DepositionAug 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: 2-dehydro-3-deoxyphosphooctonate aldolase


Theoretical massNumber of molelcules
Total (without water)30,8711
Polymers30,8711
Non-polymers00
Water362
1
A: 2-dehydro-3-deoxyphosphooctonate aldolase

A: 2-dehydro-3-deoxyphosphooctonate aldolase

A: 2-dehydro-3-deoxyphosphooctonate aldolase

A: 2-dehydro-3-deoxyphosphooctonate aldolase


Theoretical massNumber of molelcules
Total (without water)123,4834
Polymers123,4834
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area14270 Å2
ΔGint-81 kcal/mol
Surface area36560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.000, 118.000, 118.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein 2-dehydro-3-deoxyphosphooctonate aldolase / 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase / KDO-8-phosphate synthase / KDOPS / Phospho- ...3-deoxy-D-manno-octulosonic acid 8-phosphate synthase / KDO-8-phosphate synthase / KDOPS / Phospho-2-dehydro-3-deoxyoctonate aldolase


Mass: 30870.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain B / BL21-DE3) (bacteria)
Strain: B / BL21-DE3 / Gene: kdsA, ECBD_2406 / Plasmid: pET-23d / Production host: Escherichia coli (E. coli)
References: UniProt: A0A140N8Q6, UniProt: P0A715*PLUS, 3-deoxy-8-phosphooctulonate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.47 %
Description: uniform crystals ranging between 8 and 10 micrometers
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.3
Details: 8.75-12 mg/mL KDO8PS in 20 mM Tris-HCl pH=7.3, 125 mM KCl, 2 mM beta-mercaptoethanol with 16-20% w/v poly(ethylene glycol) methyl ether

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.3316 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Sep 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3316 Å / Relative weight: 1
ReflectionResolution: 2.8→48 Å / Num. obs: 6888 / % possible obs: 100 % / Redundancy: 184.2 % / Biso Wilson estimate: 84.6 Å2 / CC1/2: 0.6367 / R split: 0.143 / Net I/σ(I): 4.61
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 147.4 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 674 / CC1/2: 0.4168 / R split: 1.212 / % possible all: 100
Serial crystallography measurementFocal spot size: 300 µm2 / Pulse duration: 100 fsec. / Pulse energy: 280 µJ / Pulse photon energy: 9.3 keV / XFEL pulse repetition rate: 320 Hz
Serial crystallography sample deliveryDescription: droplet in oil / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: fluorinated oil / Description: droplet in oil GDVN infection / Flow rate: 8 µL/min / Jet diameter: 7.5 µm

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
CrystFEL0.8.0data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X8F

1x8f


Resolution: 2.8→48 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 24.441 / SU ML: 0.432 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 655 9.5 %RANDOM
Rwork0.1864 ---
obs0.1924 6223 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 243.25 Å2 / Biso mean: 89.936 Å2 / Biso min: 44.23 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.8→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 0 2 2090
Biso mean---72.65 -
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132139
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172056
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.6352888
X-RAY DIFFRACTIONr_angle_other_deg1.1621.5794786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1175273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.62524.08298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.23715383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.963158
X-RAY DIFFRACTIONr_chiral_restr0.0570.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022386
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02406
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 48 -
Rwork0.374 439 -
all-487 -
obs--100 %

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