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- PDB-2yes: Crystal Structure of Rv0371C complex with Manganese from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 2yes
TitleCrystal Structure of Rv0371C complex with Manganese from Mycobacterium Tuberculosis H37Rv
ComponentsMOCA-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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCho, H.J. / kang, B.S.
CitationJournal: To be Published
Title: Crystal Structure of Rv0371C Complex with Manganese from Mycobacterium Tuberculosis H37Rv
Authors: Cho, H.J. / Kang, B.S.
History
DepositionMar 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2011Provider: 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_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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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: MOCA-RELATED PROTEIN
B: MOCA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7037
Polymers42,3172
Non-polymers3865
Water3,675204
1
A: MOCA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3053
Polymers21,1581
Non-polymers1472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MOCA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3974
Polymers21,1581
Non-polymers2393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.220, 59.697, 146.379
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 MOCA-RELATED PROTEIN


Mass: 21158.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SER16-THR21 DISORDERED REGION / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PGST PARALLEL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53706
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.18 Å3/Da / Density % sol: 43.57 % / Description: NONE
Crystal growDetails: 18% (V/V) PEG 4000, 0.1 M MES (PH 6.0) BY MICROSEEDING

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Jun 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 30184 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 31.27
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.76 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WEE

2wee


Resolution: 1.9→50.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.607 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 16-21, 76-81 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23533 1521 5.1 %RANDOM
Rwork0.20346 ---
obs0.20507 28485 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.651 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--1.1 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 20 204 2968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222827
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8451.9653851
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8585.108372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22822.222108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1115423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0481527
X-RAY DIFFRACTIONr_chiral_restr0.0530.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212101
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_it0.67631833
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27252934
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.038994
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.25811915
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: 1.896→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 105 -
Rwork0.144 2022 -
obs--97.93 %
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)
11.3046-0.2654-0.33791.4057-0.34392.25820.01880.1-0.0007-0.2876-0.0306-0.03180.07050.00950.01180.06020.00220.01040.0139-0.01460.056516.1328-1.9945-31.2197
21.8621-0.21180.13821.52280.41621.9245-0.0824-0.22070.09570.24560.0998-0.05920.08280.0151-0.01740.04220.0195-0.00470.0349-0.02580.0595-4.70230.6109-2.6362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 195
2X-RAY DIFFRACTION2B2 - 194

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