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- PDB-1tuh: Structure of Bal32a from a Soil-Derived Mobile Gene Cassette -

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Basic information

Entry
Database: PDB / ID: 1tuh
TitleStructure of Bal32a from a Soil-Derived Mobile Gene Cassette
Componentshypothetical protein EGC068
KeywordsUNKNOWN FUNCTION / uncultured
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / ACETATE ION / SnoaL-like domain-containing protein
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.85 Å
AuthorsRobinson, A. / Wu, P.S.-C. / Harrop, S.J. / Schaeffer, P.M. / Dixon, N.E. / Gillings, M.R. / Holmes, A.J. / Nevalainen, K.M.H. / Otting, G. / Stokes, H.W. ...Robinson, A. / Wu, P.S.-C. / Harrop, S.J. / Schaeffer, P.M. / Dixon, N.E. / Gillings, M.R. / Holmes, A.J. / Nevalainen, K.M.H. / Otting, G. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Integron-associated Mobile Gene Cassettes Code for Folded Proteins: The Structure of Bal32a, a New Member of the Adaptable alpha+beta Barrel Family
Authors: Robinson, A. / Wu, P.S.-C. / Harrop, S.J. / Schaeffer, P.M. / Dosztanyi, Z. / Gillings, M.R. / Holmes, A.J. / Nevalainen, K.M.H. / Stokes, H.W. / Otting, G. / Dixon, N.E. / Curmi, P.M.G. / Mabbutt, B.C.
History
DepositionJun 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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 EGC068
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8272
Polymers17,7681
Non-polymers591
Water1,35175
1
A: hypothetical protein EGC068
hetero molecules

A: hypothetical protein EGC068
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6544
Polymers35,5362
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)60.728, 60.728, 89.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe second part of the biological assembly is generated by the two fold axis: y, x, 1-z.

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Components

#1: Protein hypothetical protein EGC068 / Bal32a


Mass: 17767.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: EGC068 / Plasmid: pETMCIII / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q99IU3
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 25, 2003 / Details: mirrors
RadiationMonochromator: RIGAKU MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→22.5 Å / Num. all: 14962 / Num. obs: 14962 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.898 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 1.85→22.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.605 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21213 758 5.1 %RANDOM
Rwork0.18548 ---
all0.18689 14962 --
obs0.18689 14962 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.676 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→22.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 0 4 75 1147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211097
X-RAY DIFFRACTIONr_bond_other_d0.0020.02954
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.9011474
X-RAY DIFFRACTIONr_angle_other_deg0.92432195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.355130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68222.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59915177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5211513
X-RAY DIFFRACTIONr_chiral_restr0.1240.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02276
X-RAY DIFFRACTIONr_nbd_refined0.210.2201
X-RAY DIFFRACTIONr_nbd_other0.2030.2940
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2522
X-RAY DIFFRACTIONr_nbtor_other0.0850.2657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0950.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.9821.5834
X-RAY DIFFRACTIONr_mcbond_other0.3851.5280
X-RAY DIFFRACTIONr_mcangle_it2.23721017
X-RAY DIFFRACTIONr_scbond_it3.1093539
X-RAY DIFFRACTIONr_scangle_it4.4254.5457
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 1.85 Å / Num. reflection Rwork: 1034 / Total num. of bins used: 20

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