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- PDB-1w94: Crystal Structure of Mil (Mth680), an archaeal Imp4-like protein -

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Basic information

Entry
Database: PDB / ID: 1w94
TitleCrystal Structure of Mil (Mth680), an archaeal Imp4-like protein
ComponentsPROBABLE BRIX-DOMAIN RIBOSOMAL BIOGENESIS PROTEIN
KeywordsARCHAEAL IMP4-BRIX DOMAIN / IMP4 DOMAIN / BRIX DOMAIN / RNA-BINDING PROTEIN
Function / homology
Function and homology information


rRNA processing / rRNA binding
Similarity search - Function
Probable Brix domain-containing ribosomal biogenesis protein / Brix domain / Brix domain / Brix domain profile. / Brix / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable Brix domain-containing ribosomal biogenesis protein
Similarity search - Component
Biological speciesMETHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsNg, C.L. / Antson, A.A. / Ortiz-Lombardia, M.
CitationJournal: Embo Rep. / Year: 2005
Title: Crystal Structure of Mil (Mth680): Internal Duplication and Similarity between the Imp4/Brix Domain and the Anticodon-Binding Domain of Class Iia Aminoacyl-tRNA Synthetases
Authors: Ng, C.L. / Waterman, D. / Koonin, E.V. / Antson, A.A. / Ortiz-Lombardia, M.
History
DepositionOct 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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: PROBABLE BRIX-DOMAIN RIBOSOMAL BIOGENESIS PROTEIN
B: PROBABLE BRIX-DOMAIN RIBOSOMAL BIOGENESIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)36,1832
Polymers36,1832
Non-polymers00
Water2,468137
1
A: PROBABLE BRIX-DOMAIN RIBOSOMAL BIOGENESIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,0921
Polymers18,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROBABLE BRIX-DOMAIN RIBOSOMAL BIOGENESIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,0921
Polymers18,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)33.673, 77.533, 60.965
Angle α, β, γ (deg.)90.00, 100.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROBABLE BRIX-DOMAIN RIBOSOMAL BIOGENESIS PROTEIN / MIL


Mass: 18091.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Strain: DELTA H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O26776
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBRIX DOMAIN INVOLVED IN RIBOSOME BIOGENESIS.
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 Å3/Da / Density % sol: 38 %
Crystal growpH: 7.5
Details: THE PROTEIN AT APPROX. 10 MG/ML WAS CRYSTALLIZED IN 20% PEG3350 AND 0.1 M HEPES 7.5, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97935, 0.9795, 0.976565
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.97951
30.9765651
ReflectionResolution: 2→47.46 Å / Num. obs: 20938 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.23
Reflection shellResolution: 2→2.02 Å / Redundancy: 3.87 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.47 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2→60.08 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.816 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1074 5.1 %RANDOM
Rwork0.198 ---
obs0.2 19845 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: 31.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-0.27 Å2
2---0.24 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2→60.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 0 137 2560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222470
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9713316
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6575300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66321.121116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.02315454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1851538
X-RAY DIFFRACTIONr_chiral_restr0.1180.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021868
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.21012
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21675
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1741.51554
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35222417
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4831037
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7674.5899
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.325 87
Rwork0.27 1449
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.95260.13340.35471.92230.28931.66460.0172-0.05370.0826-0.06-0.04340.14240.0214-0.10120.0261-0.1305-0.00580.0031-0.1360.0067-0.13883.0303-17.329-24.2262
24.05060.08751.15813.12240.39033.94810.0573-0.4739-0.50830.37020.0018-0.11930.2565-0.1909-0.0591-0.0326-0.0533-0.00920.01660.0851-0.061613.8334-26.59791.1769
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 154
2X-RAY DIFFRACTION2B1 - 154

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