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- PDB-3olq: The crystal structure of a universal stress protein E from Proteu... -

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Basic information

Entry
Database: PDB / ID: 3olq
TitleThe crystal structure of a universal stress protein E from Proteus mirabilis HI4320
ComponentsUniversal stress protein E
Keywordsstructural genomics / unknown function / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


Rossmann fold - #12370 / UspA / Universal stress protein family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Unknown ligand / Universal stress protein E
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.816 Å
AuthorsTan, K. / Chhor, G. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a universal stress protein E from Proteus mirabilis HI4320
Authors: Tan, K. / Chhor, G. / Bearden, J. / Joachimiak, A.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_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: Universal stress protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9006
Polymers36,5511
Non-polymers3495
Water4,846269
1
A: Universal stress protein E
hetero molecules

A: Universal stress protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,80112
Polymers73,1022
Non-polymers69910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9070 Å2
ΔGint-39 kcal/mol
Surface area26770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.655, 108.655, 74.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

DetailsExperimentally unknown. It is predicted that the chain A and its symmetry-related molecule (y,x,-z) may form a dimer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Universal stress protein E


Mass: 36550.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Strain: HI4320 / Gene: PMI1202, uspE / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B4ETT2

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Non-polymers , 5 types, 274 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 59.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.4M NaH2PO4/1.6M K2HPO4, 0.1M imidazole, 0.2M NaCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.816→34.5 Å / Num. all: 40612 / Num. obs: 40612 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 31.6
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1982 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.816→34.36 Å / SU ML: 0.16 / σ(F): 0.06 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 1961 5.01 %random
Rwork0.1712 ---
all0.1724 39174 --
obs0.1724 39174 96.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.944 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2459 Å2-0 Å20 Å2
2---2.2459 Å2-0 Å2
3---4.4918 Å2
Refinement stepCycle: LAST / Resolution: 1.816→34.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 78 269 2801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072594
X-RAY DIFFRACTIONf_angle_d0.9963526
X-RAY DIFFRACTIONf_dihedral_angle_d19.1021019
X-RAY DIFFRACTIONf_chiral_restr0.07390
X-RAY DIFFRACTIONf_plane_restr0.005445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8162-1.88110.25931670.213317X-RAY DIFFRACTION87
1.8811-1.95640.25411870.19173448X-RAY DIFFRACTION92
1.9564-2.04540.2261830.17563625X-RAY DIFFRACTION95
2.0454-2.15320.18892180.1633648X-RAY DIFFRACTION96
2.1532-2.28810.18361870.15343750X-RAY DIFFRACTION98
2.2881-2.46470.18831830.173801X-RAY DIFFRACTION99
2.4647-2.71270.20912000.18413822X-RAY DIFFRACTION99
2.7127-3.1050.2412140.19653850X-RAY DIFFRACTION99
3.105-3.91110.1912220.16653886X-RAY DIFFRACTION99
3.9111-34.36590.15762000.15454066X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 22.3563 Å / Origin y: 21.2465 Å / Origin z: 14.1598 Å
111213212223313233
T0.1805 Å20.026 Å20.0225 Å2-0.2105 Å20.0268 Å2--0.1701 Å2
L0.8829 °2-0.8645 °20.3918 °2-1.2195 °2-0.3003 °2--0.0184 °2
S-0.0962 Å °-0.1696 Å °-0.0455 Å °0.1374 Å °0.1365 Å °0.0337 Å °-0.0542 Å °-0.0543 Å °-0.0349 Å °
Refinement TLS groupSelection details: chain A

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