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- PDB-4wny: Crystal structure of a protein from the universal stress protein ... -

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Basic information

Entry
Database: PDB / ID: 4wny
TitleCrystal structure of a protein from the universal stress protein family from Burkholderia pseudomallei
ComponentsUniversal stress protein
KeywordsSIGNALING PROTEIN / SSGCID / Burkholderia pseudomallei / universal stress protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyUniversal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Universal stress protein family
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a protein from the universal stress protein family from Burkholderia pseudomallei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionOct 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Universal stress protein


Theoretical massNumber of molelcules
Total (without water)17,9211
Polymers17,9211
Non-polymers00
Water39622
1
A: Universal stress protein

A: Universal stress protein


Theoretical massNumber of molelcules
Total (without water)35,8412
Polymers35,8412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area1760 Å2
ΔGint-18 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.260, 79.260, 39.640
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Detailsbiological unit is a dimer generated from the monomer in the asymmetric unit by the operation: -X+2, -X+Y+1, -Z+1/3

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Components

#1: Protein Universal stress protein /


Mass: 17920.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_A2430 / Plasmid: BupsA.17310.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JFS3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Rigaku Reagents JCSG+ screen, b10: 50% PEG 200, 200mM MgCl2, 100mM Na-cacodylate pH 6.5; BupsA.17310.a.A1.PW31024 at 28.5mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978726 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 2, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978726 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 6890 / Num. obs: 6890 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 7.48 % / Biso Wilson estimate: 35.86 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.069 / Χ2: 0.964 / Net I/σ(I): 22.26 / Num. measured all: 51565
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.25-2.317.40.9060.5013.7537765085080.538100
2.31-2.370.940.4524.2336944974870.48598
2.37-2.440.9480.3735.2135784794790.401100
2.44-2.520.9410.3316.2135434774670.35597.9
2.52-2.60.970.2457.9535494754740.26399.8
2.6-2.690.9790.2248.7331804314190.2497.2
2.69-2.790.990.16811.5231244184180.18100
2.79-2.90.9930.13913.4731574244120.14997.2
2.9-3.030.9950.10617.228753923860.11498.5
3.03-3.180.9960.08222.3528823873810.08898.4
3.18-3.350.9980.06726.0626103573450.07296.6
3.35-3.560.9990.04835.2626153513490.05299.4
3.56-3.80.9990.04838.123143193080.05296.6
3.8-4.110.9990.03544.4321903042940.03896.7
4.11-4.510.03152.2520032792680.03396.1
4.5-5.030.9990.02857.6518502602500.0396.2
5.03-5.810.9990.03250.6116032272170.03495.6
5.81-7.120.9990.0350.8314342011940.03296.5
7.12-10.060.9990.02366.8510401611480.02591.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.537
Highest resolutionLowest resolution
Rotation39.63 Å2.62 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
MOLREPphasing
ARPmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: balbes, 1mjh

1mjh


Resolution: 2.25→39.63 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 371 5.39 %Random selection
Rwork0.2235 6517 --
obs0.2238 6888 97.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.56 Å2 / Biso mean: 50.1391 Å2 / Biso min: 22.31 Å2
Refinement stepCycle: final / Resolution: 2.25→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms953 0 0 22 975
Biso mean---39.63 -
Num. residues----132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002965
X-RAY DIFFRACTIONf_angle_d0.4891310
X-RAY DIFFRACTIONf_chiral_restr0.017159
X-RAY DIFFRACTIONf_plane_restr0.003171
X-RAY DIFFRACTIONf_dihedral_angle_d12.877341
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2501-2.57560.3123920.25562187227999
2.5756-3.24480.25691420.26122144228698
3.2448-39.63610.20091370.19982186232396
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)
15.74532.6851-0.11645.36220.76354.87360.2616-0.14460.41990.15310.04040.196-0.30610.4333-0.20670.1469-0.02240.02190.3243-0.02040.303655.017622.69227.7657
23.036-0.5147-0.59712.37370.54760.8920.1299-0.1927-0.32760.272-0.29290.7210.6249-0.04020.17740.4639-0.01530.00630.28780.01440.211545.61438.81439.3497
33.62542.37610.04853.3292-0.0062.0103-0.11720.6333-0.8262-0.26610.1626-0.93090.44960.3194-0.13420.4030.04660.06440.4179-0.0630.546859.740813.88722.0788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 39 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 84 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 147 )A0

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