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- PDB-2wny: Structure of Mth689, a DUF54 protein from Methanothermobacter the... -

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Basic information

Entry
Database: PDB / ID: 2wny
TitleStructure of Mth689, a DUF54 protein from Methanothermobacter thermautotrophicus
ComponentsCONSERVED PROTEIN MTH689Conservation
KeywordsUNKNOWN FUNCTION / EXOSOME SUPEROPERON
Function / homologyUncharacterised protein family UPF0201 / RNA binding / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / 2-Layer Sandwich / Alpha Beta / NICKEL (II) ION / Conserved protein
Function and homology information
Biological speciesMETHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNg, C.L. / Waterman, D.G. / Lebedev, A.A. / Smits, C. / Ortiz-Lombardia, M. / Antson, A.A.
CitationJournal: To be Published
Title: Structure of Mth689, a Duf54 Protein from Methanothermobacter Thermautotrophicus
Authors: Ng, C.L. / Waterman, D.G. / Lebedev, A.A. / Smits, C. / Ortiz-Lombardia, M. / Antson, A.A.
History
DepositionJul 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: CONSERVED PROTEIN MTH689
B: CONSERVED PROTEIN MTH689
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1084
Polymers33,0142
Non-polymers942
Water2,846158
1
A: CONSERVED PROTEIN MTH689
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5662
Polymers16,5071
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CONSERVED PROTEIN MTH689
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5422
Polymers16,5071
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.576, 61.021, 88.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CONSERVED PROTEIN MTH689 / Conservation / MTH_689


Mass: 16506.861 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Strain: DELTA H / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA (BL21) / References: UniProt: O26785
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 11 TO CYS ENGINEERED RESIDUE IN CHAIN B, ARG 11 TO CYS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.2M LISO4, 0.1M HEPES PH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 24137 / % possible obs: 99.9 % / Observed criterion σ(I): 2.9 / Redundancy: 6.2 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OGK

2ogk


Resolution: 1.95→24.23 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.05 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24705 515 2.1 %RANDOM
Rwork0.19104 ---
obs0.19227 23631 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å20 Å2
2--0.69 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 2 158 2406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222351
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9673166
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6785285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63322.672131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02815448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2261534
X-RAY DIFFRACTIONr_chiral_restr0.090.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211828
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4851.51397
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.39722259
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.7884.5954
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.8736.75907
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: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 41 -
Rwork0.264 1703 -
obs--100 %
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)
119.0197-12.7951-3.351111.12542.61753.38850.14540.28450.0725-0.2781-0.23180.2685-0.2377-0.37370.08650.1510.0055-0.00150.17820.00990.07344.426913.430422.7036
22.5878-2.4431-1.8946.91972.99082.427-0.1063-0.0964-0.07770.4214-0.09090.3350.1506-0.20520.19720.1853-0.04080.01670.1507-0.02960.082216.34562.04223.4779
37.5049-2.5746-1.2723.77851.96626.93470.21630.35161.0902-0.482-0.1441-0.2404-0.5304-0.2345-0.07220.28690.06380.03290.15660.0830.32919.427820.521916.5822
47.4796-2.8925-0.97233.70850.76191.49760.23540.8908-0.088-0.4615-0.35130.4692-0.1114-0.450.11590.28150.0656-0.04230.3015-0.0140.18714.960211.972712.8904
55.6933.8516-2.89775.8944-4.1274.82440.3749-0.7404-0.2690.4102-0.5486-0.174-0.20230.22080.17370.1539-0.0514-0.00130.16450.00490.135124.293719.99839.9858
65.31663.2452-1.75854.878-2.4735.3250.3235-0.28970.36530.2109-0.23310.35-0.1868-0.1326-0.09050.10830.01780.01890.0948-0.03680.138123.415524.932434.7247
71.9897-0.7182-0.02514.4669-0.25938.50270.0322-0.0449-0.0936-0.4310.0017-0.63411.06910.5994-0.03390.33290.0120.09730.1410.03840.304530.88197.719443.7103
80.77121.0712-1.3012.692-4.19817.2499-0.0129-0.1396-0.1784-0.0574-0.285-0.2690.24290.26860.29790.1439-0.00280.0080.15350.05090.223729.937212.367544.8316
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 13
2X-RAY DIFFRACTION2A14 - 59
3X-RAY DIFFRACTION3A60 - 78
4X-RAY DIFFRACTION4A79 - 137
5X-RAY DIFFRACTION5B3 - 17
6X-RAY DIFFRACTION6B18 - 61
7X-RAY DIFFRACTION7B62 - 86
8X-RAY DIFFRACTION8B87 - 138

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