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- PDB-3h92: The crystal structure of one domain of the protein with unknown f... -

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Basic information

Entry
Database: PDB / ID: 3h92
TitleThe crystal structure of one domain of the protein with unknown function from Methanocaldococcus jannaschii
ComponentsUncharacterized ATP-binding protein MJECL15
Keywordsstructural genomics / unknown function / Protein with unknown function / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


: / Uncharacterized ATP-binding protein MJ1010-like, C-terminal domain / ATPase domain / ATPase domain predominantly from Archaea / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-PG6 / Uncharacterized ATP-binding protein MJECL15
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhang, R. / Hatzos, C. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of one domain of the protein with unknown function from Methanocaldococcus jannaschii
Authors: Zhang, R. / Hatzos, C. / Moy, S. / Joachimiak, A.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 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 ATP-binding protein MJECL15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4982
Polymers11,2321
Non-polymers2661
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.501, 50.501, 42.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsThis protein exists as monomer.

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Components

#1: Protein Uncharacterized ATP-binding protein MJECL15


Mass: 11231.930 Da / Num. of mol.: 1 / Fragment: residues 274-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: GI:1522655, MJECL15 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q60277
#2: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.05M Imidazole, 20%(w/v)PEG6000, pH 8.0, 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: 0.9794, 0.9796
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 2.2→50.51 Å / Num. all: 5265 / Num. obs: 5212 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 30.46
Reflection shellResolution: 2.2→2.257 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.53 / Num. unique all: 399 / % possible all: 94.49

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→50.51 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.92 / SU B: 19.104 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.277 / ESU R Free: 0.244
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27783 238 4.4 %RANDOM
Rwork0.20216 ---
obs0.20577 5212 99 %-
all-5265 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å20 Å2
2---1.98 Å20 Å2
3---3.95 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms735 0 10 36 781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022756
X-RAY DIFFRACTIONr_bond_other_d0.0010.02553
X-RAY DIFFRACTIONr_angle_refined_deg1.7622.0141009
X-RAY DIFFRACTIONr_angle_other_deg0.9731359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.244585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.9525.52638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.95715162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.905154
X-RAY DIFFRACTIONr_chiral_restr0.0920.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02787
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02136
X-RAY DIFFRACTIONr_mcbond_it1.0141.5430
X-RAY DIFFRACTIONr_mcbond_other0.2091.5170
X-RAY DIFFRACTIONr_mcangle_it1.9552698
X-RAY DIFFRACTIONr_scbond_it3.1053326
X-RAY DIFFRACTIONr_scangle_it5.3594.5311
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 21 -
Rwork0.242 356 -
obs-377 94.49 %
Refinement TLS params.Method: refined / Origin x: 13.628 Å / Origin y: 10.268 Å / Origin z: 37.98 Å
111213212223313233
T0.0696 Å2-0.0308 Å2-0.0178 Å2-0.0352 Å20.034 Å2--0.1401 Å2
L4.1958 °2-1.0813 °2-0.3035 °2-2.8616 °20.1325 °2--2.7204 °2
S-0.0169 Å °-0.0244 Å °0.2607 Å °-0.1248 Å °0.0869 Å °-0.058 Å °-0.0783 Å °0.0775 Å °-0.07 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 18
2X-RAY DIFFRACTION1A19 - 30
3X-RAY DIFFRACTION1A31 - 40
4X-RAY DIFFRACTION1A41 - 50
5X-RAY DIFFRACTION1A51 - 60
6X-RAY DIFFRACTION1A61 - 70
7X-RAY DIFFRACTION1A71 - 80
8X-RAY DIFFRACTION1A81 - 92

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