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- PDB-2wee: Crystal structure of Rv0371c from Mycobacterium tuberculosis H37Rv -

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Basic information

Entry
Database: PDB / ID: 2wee
TitleCrystal structure of Rv0371c from Mycobacterium tuberculosis H37Rv
ComponentsMOBA-RELATED PROTEIN
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


nucleotidyltransferase activity / metal ion binding
Similarity search - Function
MobA-like NTP transferase / MobA-like NTP transferase domain / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
MobA-like NTP transferase domain-containing protein
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS H37RV (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCho, H.J. / Kang, B.S.
CitationJournal: To be Published
Title: Crystal Structure of Rv0371C from Mycobacterium Tuberculosis H37Rv
Authors: Cho, H.J. / Kang, B.S.
History
DepositionMar 29, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MOBA-RELATED PROTEIN
B: MOBA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5014
Polymers42,3172
Non-polymers1842
Water6,089338
1
A: MOBA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2502
Polymers21,1581
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MOBA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2502
Polymers21,1581
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.219, 61.019, 143.386
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 MOBA-RELATED PROTEIN


Mass: 21158.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) MYCOBACTERIUM TUBERCULOSIS H37RV (bacteria)
References: UniProt: O53706
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M MES PH 6.0 AND 18% PEG 4000 BY MICRO-SEEDING

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 12, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 40721 / % possible obs: 89.4 % / Observed criterion σ(I): 1.65 / Redundancy: 7.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.36 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WE9

2we9


Resolution: 1.65→31.25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.168 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2053 5.1 %RANDOM
Rwork0.211 ---
obs0.214 38549 89.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.12 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.65→31.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 0 12 338 3222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223061
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.9614193
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.3025.096417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13921.328128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9915484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7981539
X-RAY DIFFRACTIONr_chiral_restr0.0790.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022325
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21431
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22072
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.56531988
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.45753139
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.88981194
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.588111037
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: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 155 -
Rwork0.278 3102 -
obs--98.4 %
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)
10.7173-0.15790.66010.5725-0.07921.7576-0.00610.10620.0039-0.08390.02790.052-0.00450.0547-0.0218-0.0074-0.0086-0.0088-0.03470.0479-0.02287.4061.63440.443
21.0264-0.1919-0.27580.5761-0.00041.5287-0.0429-0.11120.02960.09860.05030.0327-0.00270.0699-0.00730.00890.01040.0041-0.07880.0312-0.022428.022-1.21170.266
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 194
2X-RAY DIFFRACTION2B2 - 194

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