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- PDB-3tnj: Crystal structure of universal stress protein from Nitrosomonas e... -

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Basic information

Entry
Database: PDB / ID: 3tnj
TitleCrystal structure of universal stress protein from Nitrosomonas europaea with AMP bound
ComponentsUniversal stress protein (Usp)
KeywordsCHAPERONE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / universal stress protein
Function / homology
Function and homology information


nucleotide binding / cytoplasm
Similarity search - Function
Universal 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
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Universal stress protein
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTkaczuk, K.L. / Chruszcz, M. / Shumilin, I.A. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Evol Appl / Year: 2013
Title: Structural and functional insight into the universal stress protein family.
Authors: Tkaczuk, K.L. / Shumilin, I.A. / Chruszcz, M. / Evdokimova, E. / Savchenko, A. / Minor, W.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 13, 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 (Usp)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9632
Polymers16,6161
Non-polymers3471
Water64936
1
A: Universal stress protein (Usp)
hetero molecules

A: Universal stress protein (Usp)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9264
Polymers33,2322
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area3210 Å2
ΔGint-7 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.809, 77.809, 39.949
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Detailsdimer

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Components

#1: Protein Universal stress protein (Usp)


Mass: 16615.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Strain: ATCC 19718 / Gene: NE1028 / Plasmid: P15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) / References: UniProt: Q82VN8
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M BisTris PH 7.0, 46% PEGP400, 6% Xylitol,10mM AMP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 15, 2011 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 9070 / Num. obs: 9070 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 29
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2 / Num. unique all: 470 / Rsym value: 0.575 / % possible all: 97.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.6.0117refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2PFS

2pfs


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.595 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24081 433 4.8 %RANDOM
Rwork0.18906 ---
all0.1913 8637 --
obs0.1913 8637 93.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.787 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-1.04 Å20 Å2
2---2.08 Å20 Å2
3---3.12 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 0 23 36 1055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191035
X-RAY DIFFRACTIONr_bond_other_d0.0060.02649
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9761412
X-RAY DIFFRACTIONr_angle_other_deg0.99131593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81624.66745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69115167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.288156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021130
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02195
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 33 -
Rwork0.238 592 -
obs--95.86 %
Refinement TLS params.Method: refined / Origin x: -24.234 Å / Origin y: -12.745 Å / Origin z: -8.408 Å
111213212223313233
T0.1493 Å2-0.0116 Å20.0048 Å2-0.1913 Å20.0242 Å2--0.0302 Å2
L1.6345 °20.1191 °20.3223 °2-3.9417 °21.2651 °2--1.6388 °2
S-0.0729 Å °0.0726 Å °-0.0247 Å °-0.1062 Å °0.1138 Å °-0.3035 Å °-0.0084 Å °0.2538 Å °-0.0409 Å °

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