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- PDB-3mt0: The crystal structure of a functionally unknown protein PA1789 fr... -

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Basic information

Entry
Database: PDB / ID: 3mt0
TitleThe crystal structure of a functionally unknown protein PA1789 from Pseudomonas aeruginosa PAO1
Componentsuncharacterized protein PA1789
Keywordsstructural genomics / unknown function / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyRossmann fold - #12370 / UspA / Universal stress protein family / Rossmann fold / 3-Layer(aba) Sandwich / cytoplasm / Alpha Beta / UspA domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.582 Å
AuthorsTan, K. / Chang, C. / Tesar, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally unknown protein PA1789 from Pseudomonas aeruginosa PAO1
Authors: Tan, K. / Chang, C. / Tesar, C. / Bearden, J. / Joachimiak, A.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 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: uncharacterized protein PA1789
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8314
Polymers31,7251
Non-polymers1063
Water3,999222
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.749, 67.227, 48.446
Angle α, β, γ (deg.)90.00, 110.97, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. It is likely the molecule is monomeric.

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Components

#1: Protein uncharacterized protein PA1789


Mass: 31724.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1789 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9I2V3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris, 20%(v/v) PEG8000, pH 8.5, 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: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.58→35 Å / Num. all: 34184 / Num. obs: 34184 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 28.5
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.45 / Num. unique all: 1613 / % possible all: 92.9

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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: 1.582→34.324 Å / SU ML: 0.17 / σ(F): 0.07 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 1661 5.06 %random
Rwork0.1761 ---
all0.1776 32797 --
obs0.1776 32797 93.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.919 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.814 Å20 Å21.7299 Å2
2--9.2903 Å20 Å2
3----7.4763 Å2
Refinement stepCycle: LAST / Resolution: 1.582→34.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 0 3 222 2382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062292
X-RAY DIFFRACTIONf_angle_d0.9423131
X-RAY DIFFRACTIONf_dihedral_angle_d15.156867
X-RAY DIFFRACTIONf_chiral_restr0.066371
X-RAY DIFFRACTIONf_plane_restr0.005408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5817-1.63820.25131580.24742734X-RAY DIFFRACTION83
1.6382-1.70380.23391820.21252895X-RAY DIFFRACTION88
1.7038-1.78140.24391520.20293032X-RAY DIFFRACTION92
1.7814-1.87530.23481580.18783141X-RAY DIFFRACTION94
1.8753-1.99280.21041730.17753180X-RAY DIFFRACTION97
1.9928-2.14660.21131620.17143237X-RAY DIFFRACTION97
2.1466-2.36260.19341770.17053246X-RAY DIFFRACTION98
2.3626-2.70430.23411550.18283239X-RAY DIFFRACTION97
2.7043-3.40670.21721750.17843251X-RAY DIFFRACTION97
3.4067-34.33180.16111690.15453181X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 9.7683 Å / Origin y: 4.8838 Å / Origin z: 33.3832 Å
111213212223313233
T0.1269 Å20.0037 Å2-0.0068 Å2-0.1047 Å20.0018 Å2--0.1099 Å2
L1.3859 °20.1106 °2-0.3252 °2-0.3914 °20.0533 °2--1.0114 °2
S-0.0103 Å °0.0308 Å °-0.0104 Å °0.0499 Å °0.0121 Å °0.0032 Å °0.056 Å °-0.0981 Å °0.0015 Å °
Refinement TLS groupSelection details: chain A

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