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- PDB-6u0o: Crystal structure of a peptidoglycan release complex, SagB-SpdC, ... -

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Basic information

Entry
Database: PDB / ID: 6u0o
TitleCrystal structure of a peptidoglycan release complex, SagB-SpdC, in lipidic cubic phase
Components
  • FLAG peptide
  • LYZ2 domain-containing protein
  • Lysostaphin resistance protein A
KeywordsHYDROLASE / Glucosaminidase / Peptidoglycan hydrolase / CAAX protease
Function / homology
Function and homology information


CAAX-box protein processing / amidase activity / metalloendopeptidase activity / extracellular region / membrane / plasma membrane
Similarity search - Function
Type II CAAX prenyl endopeptidase Rce1-like / Type II CAAX prenyl endopeptidase Rce1-like / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
Similarity search - Domain/homology
2-(2-ETHOXYETHOXY)ETHANOL / CITRATE ANION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain-containing protein / Lysostaphin resistance protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsOwens, T.W. / Schaefer, K. / Kahne, D. / Walker, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM076710-12 United States
Citation
Journal: Nat Microbiol / Year: 2021
Title: Structure and reconstitution of a hydrolase complex that may release peptidoglycan from the membrane after polymerization.
Authors: Schaefer, K. / Owens, T.W. / Page, J.E. / Santiago, M. / Kahne, D. / Walker, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionAug 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 6, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysostaphin resistance protein A
B: LYZ2 domain-containing protein
D: FLAG peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,42311
Polymers66,1263
Non-polymers1,2968
Water1,44180
1
A: Lysostaphin resistance protein A
B: LYZ2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,40810
Polymers65,1112
Non-polymers1,2968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: FLAG peptide


  • defined by author
  • 1.01 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,0151
Polymers1,0151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.669, 54.758, 96.418
Angle α, β, γ (deg.)90.000, 107.180, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Lysostaphin resistance protein A


Mass: 31024.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal FLAG tag and linker
Source: (gene. exp.) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / Gene: lyrA, SAB2212 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2YYX7
#2: Protein LYZ2 domain-containing protein


Mass: 34086.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal polyhistine tag
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: SAOUHSC_01895 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FXF4

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Protein/peptide , 1 types, 1 molecules D

#3: Protein/peptide FLAG peptide


Mass: 1014.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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Non-polymers , 6 types, 88 molecules

#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase
Details: 24-32% PEG400, 0.5M ammonium sulfate, 100mM sodium citrate or sodium acetate pH 4.4-5.0 (4.6 optimal), 35 mg/mL protein
PH range: 4.4-5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→46.98 Å / Num. obs: 24207 / % possible obs: 99.3 % / Redundancy: 5.8 % / Biso Wilson estimate: 71.78 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.097 / Net I/σ(I): 4.7
Reflection shellResolution: 2.6→2.71 Å / Rmerge(I) obs: 1.669 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2870 / CC1/2: 0.53 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDS0.85data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6fxp

6fxp


Resolution: 2.6→46.98 Å / SU ML: 0.4198 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.9573
RfactorNum. reflection% reflectionSelection details
Rfree0.2792 1763 7.33 %random selection
Rwork0.2527 ---
obs0.2546 24046 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 98.66 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4233 0 73 80 4386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254392
X-RAY DIFFRACTIONf_angle_d0.4785933
X-RAY DIFFRACTIONf_chiral_restr0.0391680
X-RAY DIFFRACTIONf_plane_restr0.0026730
X-RAY DIFFRACTIONf_dihedral_angle_d13.1642547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.44021420.41511648X-RAY DIFFRACTION96.76
2.67-2.750.35561370.37911710X-RAY DIFFRACTION99.3
2.75-2.840.38121600.36851688X-RAY DIFFRACTION99.25
2.84-2.940.39361210.32991694X-RAY DIFFRACTION98.91
2.94-3.060.32261130.3121746X-RAY DIFFRACTION99.62
3.06-3.20.38491360.30881734X-RAY DIFFRACTION99.2
3.2-3.360.31691400.29961684X-RAY DIFFRACTION99.45
3.36-3.580.32471260.271761X-RAY DIFFRACTION99.63
3.58-3.850.29521320.25521711X-RAY DIFFRACTION99.46
3.85-4.240.281260.2321727X-RAY DIFFRACTION98.67
4.24-4.850.25071490.2241658X-RAY DIFFRACTION95.66
4.85-6.110.25011350.23451751X-RAY DIFFRACTION99.11
6.11-46.980.22581460.21221771X-RAY DIFFRACTION97.66
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.320508903260.4635663016384.094533918876.4450279886-1.881400149913.99030610763-0.1076041286360.3769979537920.411919389274-0.3261065622080.333947870650.5700239769990.378498949534-1.303021469770.2865425974490.6817152749360.0242361577960.2312904386820.852791384489-0.1285378538170.588209599013-83.3501839939-12.368746419134.253444145
28.031855598643.31561099739-0.09565702314866.18588750888-0.7251426498244.04775651671.05231171468-1.285493702660.6604945181731.739023136380.1492851892390.646413091917-0.8312149824660.829799138405-1.137446259711.228137179960.06639631856190.4167388551861.09259518383-0.04440618698840.570192916757-80.1880901538-6.24701867829145.064257744
32.71669515484-0.119982272884-1.463101846575.01721066365-0.08790563793145.73230786690.633100024817-0.4001559110810.108447190390.450508746612-0.63848770812-0.151332449235-0.3281362788791.25464120169-0.06828690508630.567664828235-0.3124669053630.02168843337681.657930664740.128968816220.582472638691-57.2520805532-7.74050497373125.907398288
42.716272968372.07860971441-3.464889961323.96844108267-0.9468569841584.117632387640.413296196755-1.10652851932-0.00489925928180.885666470523-0.3564605103740.185861313636-0.1344502484080.997223563314-0.01767860804290.634379654292-0.1120426445020.008146520729911.35004605425-0.03355538998910.432022032058-66.6548295461-13.6241790418134.363597253
55.42479592528-0.7729103884166.095691548243.273491806171.513282399658.391530170240.127446920812-1.081073664810.6739621315620.832631322056-0.872679819964-0.205845026714-0.439803891421.70236167730.8536783941.18145891108-0.748623278452-0.1079193518352.04879828006-0.1252457538230.673920783798-49.4674855638-1.81202351955135.248958237
68.191058040740.861776094335-4.436244158664.61027752159-1.927644113388.269917344320.452962521247-0.1125468506220.433703388365-0.165851100005-0.4964524061050.0221057543282-0.1288916566861.542381489250.09453874492590.4366271335410.03942739819830.06416601653880.601357980433-0.08639262575890.660242928898-42.78890541893.3150618692385.4324420316
71.922274103060.939803589415-1.645322472783.63761552615-3.057941764447.203787069960.1682455466-0.1695937291360.2372656297910.01937806242920.02053327658510.338441769329-0.369373514766-0.90923331938-0.2890236705010.4901197819440.07491900182410.05124341603981.13006917834-0.1144954498820.541543288108-51.196230209-1.5343560498591.2436317033
82.263963476711.18155777371-6.301265212849.722651398441.503557317418.27473317386-0.15101770733-0.844204498979-0.78719497299-0.3287424608660.3715658213330.1296654486360.3146230111580.297810605265-0.08655221449010.5700665281630.10243381088-0.05653208769180.64466321962-0.008247721010240.530281059235-47.5729889352-14.985788171595.788914823
91.826910162970.164713210114-2.129622899918.25261851581-2.723655760114.33856862412-0.2592149033020.592835402675-0.388645575306-1.159254712380.1256087259750.569670964830.986268288235-0.6819409207410.09072993528280.635939448174-0.0378048174378-0.06373812154431.23121253142-0.1758856532580.599035408014-52.2673439934-14.226845630986.152142022
108.47300941406-0.7679685719882.72336086894.339319244572.797229533943.96177766348-0.1587635500440.1106550948510.93002139787-0.232850318377-0.3005495484450.173236194345-1.1215551851.16479379920.3773779905270.669624714772-0.161053431345-0.01948522779480.994410362082-0.0006467514486910.483776700971-33.67885725896.7936256566490.0998431888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 252 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 69 )
7X-RAY DIFFRACTION7chain 'B' and (resid 70 through 130 )
8X-RAY DIFFRACTION8chain 'B' and (resid 131 through 154 )
9X-RAY DIFFRACTION9chain 'B' and (resid 155 through 263 )
10X-RAY DIFFRACTION10chain 'B' and (resid 264 through 290 )

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