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- PDB-6cb2: Crystal structure of Escherichia coli UppP -

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Basic information

Entry
Database: PDB / ID: 6cb2
TitleCrystal structure of Escherichia coli UppP
ComponentsUndecaprenyl-diphosphatase
KeywordsHYDROLASE / Undecaprenyl / Pyrophosphate / Phosphatase
Function / homology
Function and homology information


undecaprenyl-diphosphate phosphatase / undecaprenyl-diphosphatase activity / pyrophosphatase activity / peptidoglycan metabolic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / plasma membrane
Similarity search - Function
Undecaprenyl-diphosphatase UppP / Bacitracin resistance protein BacA
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Undecaprenyl-diphosphatase / Undecaprenyl-diphosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsWorkman, S.D. / Worrall, L.J. / Strynadka, N.C.J.
CitationJournal: Nat Commun / Year: 2018
Title: Crystal structure of an intramembranal phosphatase central to bacterial cell-wall peptidoglycan biosynthesis and lipid recycling.
Authors: Workman, S.D. / Worrall, L.J. / Strynadka, N.C.J.
History
DepositionFeb 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 6, 2018Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Undecaprenyl-diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,12210
Polymers31,9551
Non-polymers2,1679
Water79344
1
A: Undecaprenyl-diphosphatase
hetero molecules

A: Undecaprenyl-diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,24420
Polymers63,9102
Non-polymers4,33418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area4390 Å2
ΔGint-141 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.880, 146.080, 40.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

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Components

#1: Protein Undecaprenyl-diphosphatase / Bacitracin resistance protein / Undecaprenyl pyrophosphate phosphatase


Mass: 31955.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: uppP, bacA, upk, b3057, JW3029 / Production host: Escherichia coli (E. coli)
References: UniProt: P60932, UniProt: P60933*PLUS, undecaprenyl-diphosphate phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 45-50% PEG 200, 0-150 mM NaCl, 200-400 mM LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→73.15 Å / Num. obs: 21698 / % possible obs: 96.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 26.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.048 / Rrim(I) all: 0.118 / Net I/σ(I): 8.1 / Num. measured all: 124700 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.053.91.58446411560.3970.8441.8041.173.1
8.94-73.155.30.026160130410.0130.0324.899.6

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
SHARPphasing
RefinementResolution: 2→73.04 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.54
RfactorNum. reflection% reflection
Rfree0.2535 1077 5 %
Rwork0.2187 --
obs0.2204 21536 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.25 Å2 / Biso mean: 46.244 Å2 / Biso min: 15.24 Å2
Refinement stepCycle: final / Resolution: 2→73.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 145 44 2261
Biso mean--67.47 41.54 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9971-2.0880.36841040.35771886199072
2.088-2.19810.37411310.31932503263495
2.1981-2.33580.32031370.27732620275799
2.3358-2.51620.29711370.24162631276899
2.5162-2.76940.27391370.207526422779100
2.7694-3.17020.22491400.199126552795100
3.1702-3.99410.21831430.18627042847100
3.9941-73.08890.21661480.194928182966100
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)
16.29472.9351.88522.9969-1.33696.13210.04940.15510.17170.15830.02160.4166-0.1963-0.5623-0.00330.48210.09590.07510.26470.03920.255920.180725.99424.6394
25.44094.6041-6.63235.8482-4.51948.35740.83851.26860.4550.5061-0.13340.3061-0.6947-1.2229-0.70290.55650.14740.02140.3833-0.00240.24222.706924.416414.2365
34.6015-1.93742.33511.6613-0.13073.5190.10770.40.4787-0.1159-0.2045-0.3632-0.40820.26360.07950.53130.0316-0.00460.22570.03750.197241.366115.22816.2994
47.7631-2.0849-0.01243.8944-0.64912.61620.19550.8328-0.46490.1915-0.02720.7683-0.1602-0.4148-0.14110.45920.090.04470.3778-0.00260.291524.0247.47626.2638
56.34941.3317-1.58912.65610.2821.617-0.1096-0.040.27360.00060.0790.04460.0542-0.21550.02630.2850.0256-0.04020.16180.02460.122939.3637.568719.3848
67.4986-1.03086.79893.4368-0.61257.78980.0935-0.71990.47990.0202-0.26590.21150.3418-1.16450.14460.37680.01790.02950.3716-0.03940.177329.801316.351912.3566
78.5847-6.39970.5548.9964-2.9184.60360.40580.60670.5801-0.3549-0.13970.30410.0792-0.6153-0.29030.49960.08770.11870.26830.0570.238525.288529.255416.0452
87.1013-1.3266-4.74521.29091.11916.93010.088-0.02120.24120.2274-0.03760.1534-0.082-0.19550.05160.54580.05890.0130.19190.02910.16428.630716.634133.6672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 41 )A4 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 63 )A42 - 63
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 108 )A64 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 139 )A109 - 139
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 188 )A140 - 188
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 215 )A189 - 215
7X-RAY DIFFRACTION7chain 'A' and (resid 216 through 249 )A216 - 249
8X-RAY DIFFRACTION8chain 'A' and (resid 250 through 273 )A250 - 273

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