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- PDB-2waw: crystal structure of Mycobacterium tuberculosis rv0371c homolog f... -

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Basic information

Entry
Database: PDB / ID: 2waw
Titlecrystal structure of Mycobacterium tuberculosis rv0371c homolog from mycobacterium sp. strain JC1
ComponentsMOBA RELATE PROTEIN
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


nucleotidyltransferase activity
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
TRIETHYLENE GLYCOL / Moba relate protein
Similarity search - Component
Biological speciesMYCOBACTERIUM SP. JC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCho, H.J. / Kang, B.S.
CitationJournal: To be Published
Title: Crystal Structure of Mycobacterium Tuberculosis Rv0371C Homolog from Mycobacterium Sp. Strain Jc1
Authors: Cho, H.J. / Kang, B.S.
History
DepositionFeb 17, 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 1.2May 1, 2024Group: 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 1.3Oct 16, 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 RELATE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3494
Polymers21,1281
Non-polymers2213
Water3,657203
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.081, 61.746, 80.059
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 RELATE PROTEIN


Mass: 21128.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MYCOBACTERIUM SP. JC-1 (bacteria) / References: UniProt: D5MNX3*PLUS
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 44.21 % / Description: NONE
Crystal growpH: 7.5
Details: 28% PEG 400, 0.1M HEPES PH 7.5, 0.2M CALCIUM CHLORIDE

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 12, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 23465 / % possible obs: 94.1 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 42.8
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.8 / % possible all: 72.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MYCOBACTERIUM TUBERCULOSIS RV0371C

Resolution: 1.6→24.5 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.247 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1254 5.1 %RANDOM
Rwork0.173 ---
obs0.175 23465 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2---0.16 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 12 203 1682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221585
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.9812172
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1265.089224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96122.38163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20515260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1191517
X-RAY DIFFRACTIONr_chiral_restr0.0830.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021194
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2727
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21068
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.59231037
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.48351628
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9488621
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.84611531
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.246 68
Rwork0.224 1485
Refinement TLS params.Method: refined / Origin x: 4.034 Å / Origin y: -4.752 Å / Origin z: -15.109 Å
111213212223313233
T-0.0567 Å2-0.0116 Å2-0.0047 Å2--0.0088 Å20.0064 Å2--0.0035 Å2
L0.3469 °2-0.057 °20.0261 °2-0.4336 °2-0.2849 °2--1.2708 °2
S0.0134 Å °-0.0153 Å °0.0149 Å °0.0029 Å °0.0001 Å °-0.0111 Å °0.0097 Å °-0.013 Å °-0.0134 Å °

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