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- PDB-3ius: The structure of a functionally unknown conserved protein from Si... -

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Basic information

Entry
Database: PDB / ID: 3ius
TitleThe structure of a functionally unknown conserved protein from Silicibacter pomeroyi DSS
Componentsuncharacterized conserved protein
Keywordsstructural genomics / unknown function / APC63810 / Silicibacter pomeroyi DSS / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyNAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID / NAD-dependent epimerase/dehydratase domain-containing protein
Function and homology information
Biological speciesRuegeria pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 Å
AuthorsTan, K. / Tesar, C. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of a functionally unknown conserved protein from Silicibacter pomeroyi DSS
Authors: Tan, K. / Tesar, C. / Freeman, L. / Joachimiak, A.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: 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 conserved protein
B: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7255
Polymers62,5712
Non-polymers1543
Water10,215567
1
A: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4404
Polymers31,2861
Non-polymers1543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)31,2861
Polymers31,2861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.736, 81.648, 58.655
Angle α, β, γ (deg.)90.00, 94.65, 90.00
Int Tables number4
Space group name H-MP1211
Detailsauthors state that the biological unit is experimentally unknown. The molecule is likely a monomer

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Components

#1: Protein uncharacterized conserved protein


Mass: 31285.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi DSS-3 (bacteria) / Strain: DSS / Gene: Silicibacter pomeroyi, SPO3755 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q5LM08
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris Hydrochloride, 25% w/v PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2009 / Details: MIRROR
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.66→40 Å / Num. obs: 62442 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 21.4
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 1.77 / % possible all: 85.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.66→39.44 Å / SU ML: 0.29 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 3140 5.05 %
Rwork0.217 --
obs0.219 62195 97.1 %
all-62195 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.44 Å2 / ksol: 0.32 e/Å3
Refinement stepCycle: LAST / Resolution: 1.66→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 10 567 4959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054517
X-RAY DIFFRACTIONf_angle_d0.9236185
X-RAY DIFFRACTIONf_dihedral_angle_d16.5861683
X-RAY DIFFRACTIONf_chiral_restr0.057673
X-RAY DIFFRACTIONf_plane_restr0.004828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6602-1.68620.41451070.40692026X-RAY DIFFRACTION73
1.6862-1.71380.40391440.3642493X-RAY DIFFRACTION90
1.7138-1.74340.34931380.32262504X-RAY DIFFRACTION92
1.7434-1.77510.35681320.32312574X-RAY DIFFRACTION93
1.7751-1.80920.35061340.30532609X-RAY DIFFRACTION95
1.8092-1.84610.3581210.30142704X-RAY DIFFRACTION97
1.8461-1.88630.31841380.2892744X-RAY DIFFRACTION99
1.8863-1.93020.32681530.27812737X-RAY DIFFRACTION99
1.9302-1.97840.33721420.27042731X-RAY DIFFRACTION100
1.9784-2.03190.31031350.25472741X-RAY DIFFRACTION100
2.0319-2.09170.31631470.23722765X-RAY DIFFRACTION100
2.0917-2.15920.29081490.22632734X-RAY DIFFRACTION100
2.1592-2.23640.27821640.21492740X-RAY DIFFRACTION100
2.2364-2.32590.24861480.21512760X-RAY DIFFRACTION100
2.3259-2.43180.29741410.22092775X-RAY DIFFRACTION100
2.4318-2.55990.26061490.22352752X-RAY DIFFRACTION100
2.5599-2.72030.31611580.21362757X-RAY DIFFRACTION100
2.7203-2.93030.25451560.22722764X-RAY DIFFRACTION100
2.9303-3.2250.25291300.20172785X-RAY DIFFRACTION100
3.225-3.69140.20371520.17812776X-RAY DIFFRACTION100
3.6914-4.64960.17591460.15322774X-RAY DIFFRACTION100
4.6496-39.45550.16581560.16212810X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 16.9615 Å / Origin y: 12.2742 Å / Origin z: -3.3149 Å
111213212223313233
T0.104 Å20.0268 Å20.0519 Å2-0.0054 Å20.0121 Å2--0.0216 Å2
L0.047 °2-0.0857 °2-0.0148 °2-0.3832 °20.0201 °2---0.0259 °2
S-0.0555 Å °-0.0143 Å °-0.0277 Å °0.2212 Å °0.0508 Å °0.0911 Å °0.0028 Å °0.0003 Å °-0.0149 Å °
Refinement TLS groupSelection details: CHAIN B

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