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- PDB-6oss: Crystal Structure of the Acyl-Carrier-Protein UDP-N-Acetylglucosa... -

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Basic information

Entry
Database: PDB / ID: 6oss
TitleCrystal Structure of the Acyl-Carrier-Protein UDP-N-Acetylglucosamine O-Acyltransferase LpxA from Proteus mirabilis
ComponentsAcyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
KeywordsTRANSFERASE / left-handed beta helix / hexapeptide repeat / acyltransferase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase / acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / lipid A biosynthetic process / cytoplasm
Similarity search - Function
Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / UDP N-acetylglucosamine O-acyltransferase, C-terminal / UDP-N-acetylglucosamine O-acyltransferase, C-terminal domain superfamily / Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat ...Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / UDP N-acetylglucosamine O-acyltransferase, C-terminal / UDP-N-acetylglucosamine O-acyltransferase, C-terminal domain superfamily / Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHITE ION / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKim, Y. / Stogios, P. / Skarina, T. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Acyl-Carrier-Protein UDP-N-Acetylglucosamine O-Acyltransferase LpxA from Proteus mirabilis
Authors: Kim, Y. / Stogios, P. / Skarina, T. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _struct_asym.entity_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
B: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
C: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,41510
Polymers87,7593
Non-polymers6557
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-123 kcal/mol
Surface area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.789, 94.507, 136.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / UDP-N-acetylglucosamine acyltransferase


Mass: 29253.107 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (strain HI4320) (bacteria)
Strain: HI4320 / Gene: lpxA, PMI2273 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21 DE3 (gold)
References: UniProt: B4F258, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 25 % PEG5K MME, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.19→77.6 Å / Num. obs: 47819 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 42.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.4
Reflection shellResolution: 2.19→2.23 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.882 / Num. unique obs: 2315 / CC1/2: 0.447

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
DIALSdata reduction
HKL-3000data reduction
xia2data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 4J09

4j09


Resolution: 2.19→44.642 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 30.55
RfactorNum. reflection% reflection
Rfree0.2564 2344 5.09 %
Rwork0.2168 --
obs0.2188 46068 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.6 Å2
Refinement stepCycle: LAST / Resolution: 2.19→44.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6114 0 34 102 6250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026330
X-RAY DIFFRACTIONf_angle_d0.4868564
X-RAY DIFFRACTIONf_dihedral_angle_d14.8793756
X-RAY DIFFRACTIONf_chiral_restr0.053958
X-RAY DIFFRACTIONf_plane_restr0.0021143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.23470.39111310.37752409X-RAY DIFFRACTION91
2.2347-2.28330.37631340.3422418X-RAY DIFFRACTION92
2.2833-2.33640.33861440.32722422X-RAY DIFFRACTION93
2.3364-2.39480.31611280.29682461X-RAY DIFFRACTION93
2.3948-2.45960.30441220.28382496X-RAY DIFFRACTION94
2.4596-2.5320.28581270.27112499X-RAY DIFFRACTION95
2.532-2.61370.31211510.26652508X-RAY DIFFRACTION95
2.6137-2.70710.2951370.25432504X-RAY DIFFRACTION96
2.7071-2.81540.25931210.2522592X-RAY DIFFRACTION97
2.8154-2.94360.27741390.25412606X-RAY DIFFRACTION98
2.9436-3.09870.30351280.25642623X-RAY DIFFRACTION98
3.0987-3.29280.31731350.24282619X-RAY DIFFRACTION99
3.2928-3.54690.27631420.23012676X-RAY DIFFRACTION99
3.5469-3.90370.22751500.19352651X-RAY DIFFRACTION99
3.9037-4.46810.20861370.15912703X-RAY DIFFRACTION100
4.4681-5.62760.2111570.16972704X-RAY DIFFRACTION99
5.6276-44.65150.22351610.18522833X-RAY DIFFRACTION99
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)
14.9086-0.8536-0.66575.6055-0.54087.49450.0805-0.18950.08210.3811-0.2982-1.5924-0.70191.1280.18550.4021-0.1144-0.05810.50540.11160.689536.6977-29.5471-26.896
25.85660.62480.96886.6233-0.10385.7591-0.0426-0.2677-0.30270.0941-0.0569-0.33360.2273-0.03210.080.24350.01340.05810.24040.00030.371125.5873-37.5014-28.2299
36.2174-1.406-1.88987.44080.08148.5298-0.2926-0.612-0.15530.71430.03750.37410.1485-0.03260.30740.32080.00590.03640.37850.0630.368918.5901-37.6225-16.0936
41.822-1.19591.61885.42491.04124.5122-0.82610.4036-1.4891-0.52920.40491.20670.394-0.76510.05970.7195-0.26520.38390.76850.02460.94838.0119-47.3886-13.2294
51.00390.1536-1.05160.9017-0.37982.0136-0.1855-0.2126-0.66150.2677-0.40350.17791.0397-0.73550.29621.1801-0.32620.62051.16190.18490.831610.9136-52.2695-3.4764
63.0762-0.21020.55586.9399-2.83461.2303-0.5344-1.3339-0.55431.28490.18350.28180.15770.29990.17111.43550.24310.26521.18120.56550.63520.7103-51.42743.5394
76.79293.56191.49126.04192.7338.94730.0632-0.22-1.54691.4082-0.4136-0.73871.40630.39510.23020.91990.21550.09130.71470.12340.67723.2371-48.8318-6.1071
82.1837-0.083-0.58162.40150.3295.0638-0.135-0.09710.29490.00010.0044-0.3403-0.4241-0.03340.11350.3898-0.0047-0.12220.27230.00690.485725.4024-11.4974-28.6032
95.6030.85361.19433.690.93134.83780.0488-0.77220.24870.9501-0.1418-0.303-0.33340.16920.09210.99310.0534-0.23340.6737-0.16370.490926.7108-4.7216-1.0254
105.3424-0.14582.16133.4156-1.24593.64770.10621.493-0.2405-1.2744-0.07030.13450.3884-0.6396-0.00250.79170.0246-0.13170.7214-0.01360.312810.995-21.4886-56.95
115.9742-0.4509-0.42423.1178-0.47345.5712-0.00730.6108-0.07-0.4994-0.06830.2608-0.0973-0.71790.050.4320.0335-0.12330.5324-0.03950.34867.9779-24.7778-44.8849
123.19980.6064-1.02689.3157-0.42473.273-0.15390.24290.1631-0.00450.1520.4207-0.1157-0.4919-0.0120.29380.0497-0.10080.5094-0.04190.36473.2725-24.4167-36.3135
133.5242-0.6604-0.00894.3543-0.29315.3439-0.4408-0.39310.07180.29570.3590.2992-0.2747-0.72890.1120.3120.0995-0.05770.6656-0.01520.4703-0.6539-22.1399-23.9605
146.8701-2.5172.28478.375-5.35436.50730.07-0.93350.9231-0.1965-0.3483-0.32720.04350.11980.22620.59540.1404-0.00650.7981-0.19210.5945-3.7295-13.6816-16.5261
152.30541.7382-2.08154.3463-0.99525.1204-0.2837-0.58960.42131.19960.461.7458-1.0882-0.7606-0.30330.55520.34820.12741.2316-0.1740.9537-15.3109-12.8696-13.003
162.7310.2611.54233.89980.04163.28650.3346-1.1610.42990.7249-0.15711.1859-0.3477-1.4277-0.02520.63520.17110.13961.5309-0.06211.0841-21.5495-22.7858-11.9509
174.5036-1.73950.45546.08570.20822.5933-0.4757-0.1696-0.1573-0.1150.36230.85410.0714-1.15380.05830.38270.09650.0641.0170.06690.564-15.0998-24.0125-20.2793
183.9753-0.72491.2517.7282-2.11193.68370.0910.2517-0.2276-1.0713-0.2132-0.77740.52710.5320.22990.5448-0.01010.21810.5431-0.12560.525530.9953-38.466-49.71
193.67020.0735-0.88126.7666-0.38884.6515-0.14090.2644-0.6647-0.4687-0.0281-0.09430.58270.02430.15310.36920.00710.07880.3019-0.04870.448525.9055-38.0793-41.1605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 67 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 126 )
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 192 )
4X-RAY DIFFRACTION4chain 'A' and (resid 193 through 208 )
5X-RAY DIFFRACTION5chain 'A' and (resid 209 through 223 )
6X-RAY DIFFRACTION6chain 'A' and (resid 224 through 242 )
7X-RAY DIFFRACTION7chain 'A' and (resid 243 through 267 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 192 )
9X-RAY DIFFRACTION9chain 'B' and (resid 193 through 267 )
10X-RAY DIFFRACTION10chain 'C' and (resid 0 through 19 )
11X-RAY DIFFRACTION11chain 'C' and (resid 20 through 82 )
12X-RAY DIFFRACTION12chain 'C' and (resid 83 through 126 )
13X-RAY DIFFRACTION13chain 'C' and (resid 127 through 187 )
14X-RAY DIFFRACTION14chain 'C' and (resid 188 through 208 )
15X-RAY DIFFRACTION15chain 'C' and (resid 209 through 223 )
16X-RAY DIFFRACTION16chain 'C' and (resid 224 through 243 )
17X-RAY DIFFRACTION17chain 'C' and (resid 244 through 267 )
18X-RAY DIFFRACTION18chain 'A' and (resid 0 through 19 )
19X-RAY DIFFRACTION19chain 'A' and (resid 20 through 66 )

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