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- PDB-4wy2: Crystal structure of universal stress protein E from Proteus mira... -

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Basic information

Entry
Database: PDB / ID: 4wy2
TitleCrystal structure of universal stress protein E from Proteus mirabilis in complex with UDP-3-O-[(3R)-3-hydroxytetradecanoyl]-N-acetyl-alpha-glucosamine
ComponentsUniversal stress protein E
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / PSI-Biology / Midwest Center for Structural Genomics
Function / homologyRossmann fold - #12370 / UspA / Universal stress protein family / Rossmann fold / 3-Layer(aba) Sandwich / cytoplasm / Alpha Beta / Chem-U20 / Universal stress protein E
Function and homology information
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShumilin, I.A. / Shabalin, I.G. / Handing, K.B. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: to be published
Title: Crystal structure of universal stress protein E from Proteus mirabilis incomplex withUDP-3-O-[(3R)-3-hydroxytetradecanoyl]-N-acetyl-alpha-glucosamine
Authors: Shumilin, I.A. / Minor, W.
History
DepositionNov 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_related.content_type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 13, 2022Group: Database references / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation_author / database_2
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms ..._audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Universal stress protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4196
Polymers36,2701
Non-polymers1,1495
Water5,729318
1
A: Universal stress protein E
hetero molecules

A: Universal stress protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,83812
Polymers72,5392
Non-polymers2,29910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8450 Å2
ΔGint-79 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.877, 107.877, 74.923
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Universal stress protein E


Mass: 36269.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Strain: HI4320 / Gene: uspE, PMI1202 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: B4ETT2

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Non-polymers , 5 types, 323 molecules

#2: Chemical ChemComp-U20 / uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-N-acetyl-D-glucosamine / (2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydrox ytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H- pyran-4-yl (3R)-3-hydroxytetradecanoate


Mass: 833.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H53N3O19P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 3 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 ul of 12 mg/ml protein in 10mM HEPES, 500mM NaCl pH 7.5 were mixed with 0.2 ul of the Quiagen Cryos Suite condition #50 (1.36 M Ammonium Sulfate, 0.085 M MES pH 6.5, 8.5% Dioxane, 15% ...Details: 0.2 ul of 12 mg/ml protein in 10mM HEPES, 500mM NaCl pH 7.5 were mixed with 0.2 ul of the Quiagen Cryos Suite condition #50 (1.36 M Ammonium Sulfate, 0.085 M MES pH 6.5, 8.5% Dioxane, 15% Glycerol) and equilibrated against the mother liquor in 96 Well 2 drop Crystallization Plate (MRC)
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 41254 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.087 / Χ2: 1.281 / Net I/av σ(I): 22.433 / Net I/σ(I): 9.5 / Num. measured all: 274114
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.836.10.8921.920170.750.3890.9760.76498.7
1.83-1.866.10.82220010.7850.3570.8990.79898.8
1.86-1.96.20.68420190.810.2970.7480.8299.3
1.9-1.946.20.55220190.8640.2390.6040.85499.6
1.94-1.986.30.43720160.9120.1880.4770.90799.2
1.98-2.036.30.34620370.9410.1490.3780.99899.4
2.03-2.086.30.28720330.9530.1230.3131.08299.7
2.08-2.136.40.23920380.9690.1010.261.18499.9
2.13-2.26.50.20620400.9740.0870.2241.316100
2.2-2.276.70.1820680.980.0760.1961.46699.9
2.27-2.356.80.15720500.9850.0650.171.389100
2.35-2.446.90.13620290.9890.0560.1481.516100
2.44-2.5570.12220730.990.050.1321.631100
2.55-2.697.10.11120610.9910.0450.121.653100
2.69-2.867.20.09720750.9930.0390.1051.544100
2.86-3.087.20.08720780.9930.0350.0941.481100
3.08-3.397.10.07821020.9950.0320.0851.683100
3.39-3.8870.06421000.9970.0260.0691.55599.9
3.88-4.886.90.05321390.9970.0210.0571.2999.7
4.88-506.50.0422590.9990.0160.0431.23298.9

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMAC5.8.0073refinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OLQ

3olq


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.2066 / WRfactor Rwork: 0.1721 / FOM work R set: 0.8453 / SU B: 4.761 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1016 / SU Rfree: 0.1003 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 2019 4.9 %RANDOM
Rwork0.1721 39066 --
obs0.1736 39066 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 189.93 Å2 / Biso mean: 35.365 Å2 / Biso min: 13.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2---1.01 Å20 Å2
3---2.01 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 73 319 2840
Biso mean--44.04 42.28 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192593
X-RAY DIFFRACTIONr_bond_other_d0.0020.022518
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9983534
X-RAY DIFFRACTIONr_angle_other_deg0.77635804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4575312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56725.043117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23415440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2731513
X-RAY DIFFRACTIONr_chiral_restr0.0860.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
X-RAY DIFFRACTIONr_mcbond_it1.1651.6741236
X-RAY DIFFRACTIONr_mcbond_other1.1661.6721235
X-RAY DIFFRACTIONr_mcangle_it1.7922.5021543
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 121 -
Rwork0.267 2617 -
all-2738 -
obs--91.02 %
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)
10.8876-0.7193-0.43511.99811.52421.6889-0.1146-0.22750.08630.2490.2034-0.16790.1129-0.0374-0.08890.1660.0558-0.03390.1911-0.02540.019-10.86-33.98812.232
21.5848-1.468-0.62754.04343.33994.4111-0.1574-0.39630.15650.36150.3858-0.46510.07540.1076-0.22840.14510.0719-0.07350.1979-0.04540.0745-2.891-36.7814.985
32.5284-0.9089-0.81382.6361.18860.6581-0.108-0.1349-0.06310.1940.02770.16040.094-0.05610.08030.16770.0522-0.01190.1949-0.01630.0146-18.136-33.64211.357
46.9850.6453-2.049410.1319-0.5573.10030.28630.06050.5828-0.3829-0.1832-0.328-0.30930.1445-0.10310.20140.0986-0.01060.1673-0.02820.0797-18.15-19.1045.276
51.8511-1.18420.21451.5132-0.20050.2371-0.1513-0.27680.04980.2090.2222-0.08410.02130.0816-0.07080.15270.0481-0.02550.2025-0.06150.037-27.257-13.53719.304
64.2781-2.06753.30952.121-2.23086.0095-0.0459-0.15050.04540.06590.1075-0.00870.0462-0.035-0.06150.129-0.01140.03110.1282-0.02580.0758-44.201-1.93815.543
73.4289-1.08970.14592.04210.22040.8116-0.103-0.05210.34860.10790.1099-0.2352-0.04160.109-0.00680.09420.0297-0.0310.1322-0.05750.0625-27.133-6.62317.857
846.602846.27792.058381.6922-6.86612.3176-1.6872-1.3285-1.46071.56392.45741.2848-0.8477-1.0186-0.77020.81450.06320.08870.9390.31360.4622-37.85-20.0356.667
93.13650.07750.55241.78470.67381.69830.03950.207-0.42160.0833-0.04510.13690.0015-0.1340.00560.06480.0562-0.02080.1582-0.08840.0921-27.36-21.21310.597
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 57
2X-RAY DIFFRACTION2A58 - 88
3X-RAY DIFFRACTION3A89 - 118
4X-RAY DIFFRACTION4A119 - 136
5X-RAY DIFFRACTION5A137 - 207
6X-RAY DIFFRACTION6A208 - 236
7X-RAY DIFFRACTION7A237 - 272
8X-RAY DIFFRACTION8A273 - 283
9X-RAY DIFFRACTION9A284 - 311

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