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- PDB-1q77: X-ray crystal structure of putative Universal Stress Protein from... -

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Basic information

Entry
Database: PDB / ID: 1q77
TitleX-ray crystal structure of putative Universal Stress Protein from Aquifex aeolicus
ComponentsHypothetical protein AQ_178
KeywordsStructural genomics / unknown function / universal stress protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyUspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Universal stress protein Aq_178
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsOsipiuk, J. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structural homolog of Universal Stress Protein from Aquifex aeolicus
Authors: Osipiuk, J. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionAug 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 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_ref_seq_dif / 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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Hypothetical protein AQ_178
B: Hypothetical protein AQ_178
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3203
Polymers31,2242
Non-polymers961
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-24 kcal/mol
Surface area13870 Å2
MethodPISA
2
A: Hypothetical protein AQ_178
B: Hypothetical protein AQ_178
hetero molecules

A: Hypothetical protein AQ_178
B: Hypothetical protein AQ_178
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6406
Polymers62,4484
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7360 Å2
ΔGint-76 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.375, 94.375, 134.542
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Hypothetical protein AQ_178 / Universal Stress Protein


Mass: 15611.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_178 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: O66565
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
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: 4.8 Å3/Da / Density % sol: 74.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9
Details: ammonium sulfate, Tris buffer, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97962 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jul 20, 2003
RadiationMonochromator: double crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97962 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 17527 / Num. obs: 17349 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.1
Reflection shellResolution: 2.7→2.8 Å / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→47.38 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 243854.86 / Data cutoff high rms absF: 243854.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1616 10.1 %RANDOM
Rwork0.22 ---
obs0.22 16040 92.6 %-
all-17312 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5929 Å2 / ksol: 0.345768 e/Å3
Displacement parametersBiso mean: 64.7 Å2
Baniso -1Baniso -2Baniso -3
1-9.92 Å20 Å20 Å2
2--9.92 Å20 Å2
3----19.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.7→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 5 32 2227
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.442 231 9.8 %
Rwork0.449 2129 -
obs--83.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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