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- PDB-3i8o: A domain of a functionally unknown protein from Methanocaldococcu... -

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Basic information

Entry
Database: PDB / ID: 3i8o
TitleA domain of a functionally unknown protein from Methanocaldococcus jannaschii DSM 2661.
ComponentsKH domain-containing protein MJ1533
KeywordsRNA BINDING PROTEIN / APC89320.5 / Methanocaldococcus jannaschii DSM 2661 / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / RNA-binding
Function / homology
Function and homology information


RNA binding / metal ion binding
Similarity search - Function
PIN domain / Type II/IV secretion system protein / Type II/IV secretion system protein / 5'-nuclease / Large family of predicted nucleotide-binding domains / PIN domain / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / PIN-like domain superfamily ...PIN domain / Type II/IV secretion system protein / Type II/IV secretion system protein / 5'-nuclease / Large family of predicted nucleotide-binding domains / PIN domain / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / PIN-like domain superfamily / K Homology domain / K homology RNA-binding domain / K homology domain superfamily, prokaryotic type / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / DI(HYDROXYETHYL)ETHER / Uncharacterized KH and PIN-domain containing protein MJ1533
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.638 Å
AuthorsTan, K. / Chhor, G. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: A domain of a functionally unknown protein from Methanocaldococcus jannaschii DSM 2661.
Authors: Tan, K. / Chhor, G. / Cobb, G. / Joachimiak, A.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KH domain-containing protein MJ1533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5768
Polymers16,1781
Non-polymers3987
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: KH domain-containing protein MJ1533
hetero molecules

A: KH domain-containing protein MJ1533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,15216
Polymers32,3562
Non-polymers79514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area3550 Å2
ΔGint-5 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.988, 87.988, 96.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-1-

CL

DetailsIt is a monomer in solution.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein KH domain-containing protein MJ1533


Mass: 16178.149 Da / Num. of mol.: 1 / Fragment: residues 27-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: Methanocaldococcus jannaschii / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q58928

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Non-polymers , 5 types, 12 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.14M CaCl2, 0.07M Sodium Acetate, 14%(v/v) Isopropanol and 30%(v/v)glycerol, pH 4.6, 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 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2009 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.638→38.12 Å / Num. all: 5822 / Num. obs: 5822 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 22.1
Reflection shellResolution: 2.65→2.71 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 2.36 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
SBC-Collectdata collection
RefinementMethod to determine structure: MAD / Resolution: 2.638→38.116 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.926 / SU ML: 0.32 / σ(F): 1.89 / Phase error: 26.55 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2587 473 4.46 %
Rwork0.1921 --
obs0.1951 5822 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.905 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso mean: 25.182 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.638→38.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 9 21 1136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081135
X-RAY DIFFRACTIONf_angle_d1.1941517
X-RAY DIFFRACTIONf_dihedral_angle_d19.966430
X-RAY DIFFRACTIONf_chiral_restr0.08176
X-RAY DIFFRACTIONf_plane_restr0.004194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6379-3.01950.26861440.23973361X-RAY DIFFRACTION98
3.0195-3.80370.31591690.17943358X-RAY DIFFRACTION100
3.8037-38.11970.22411600.18113414X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined2.74442.3117-0.93211.3937-0.38141.5733-0.08591.29451.1882-0.45860.97981.45340.6357-0.9581-0.19640.3488-0.182-0.05220.59060.27280.356739.923544.62534.3972
20.27981.6338-1.18172.3586-2.03051.25280.14460.88611.9948-0.26620.55592.279-1.0227-2.1604-0.41980.51960.010.07940.88310.48411.3827
30.54820.5120.25371.89910.44175.5186-0.49780.54970.20910.23110.66181.45571.73740.9457-0.28460.6511-0.34670.02860.67280.15550.3514
40.08760.30890.06371.2146-0.66320.68321.1425-1.37561.0921.1581-0.72911.0483-0.3653-0.8926-0.40331.2818-0.33280.67340.7499-0.37031.2618
50.86760.3866-0.79622.0264-0.81721.05550.4586-0.9422-0.70420.1404-0.1321-0.42460.3444-0.1707-0.1460.5087-0.15460.05470.40710.08580.3378
60.84881.4919-0.06592.38810.59091.1351-0.08770.3870.54720.69340.30490.44220.9528-0.1261-0.13210.416-0.09810.03650.29410.14350.1778
70.53990.4608-0.22051.27610.79350.24281.5118-0.3354-0.6637-0.1353-1.6901-1.1130.12190.1497-0.00530.3128-0.0377-0.03950.38460.18860.3301
80.04770.5505-1.5234-0.28-0.48072.26360.0910.0374-0.13170.01080.0209-0.16210.0477-0.0104-0.16930.2059-0.0409-0.01740.22270.05230.2075
Refinement TLS groupSelection details: chain A resid 148:165

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