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- PDB-6bwh: Crystal structure of Mycoibacterium tuberculosis Rv2983 in comple... -

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Basic information

Entry
Database: PDB / ID: 6bwh
TitleCrystal structure of Mycoibacterium tuberculosis Rv2983 in complex with PEP
Components2-phospho-L-lactate guanylyltransferase
KeywordsTRANSFERASE / alpha/beta structure
Function / homologyphosphoenolpyruvate guanylyltransferase / phospholactate guanylyltransferase activity / Phosphoenolpyruvate guanylyltransferase CofC / Guanylyl transferase CofC like / F420-0 metabolic process / Nucleotide-diphospho-sugar transferases / GTP binding / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvate guanylyltransferase
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsBashiri, G. / Jirgis, E.N.M. / Baker, E.N.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
CitationJournal: Nat Commun / Year: 2019
Title: A revised biosynthetic pathway for the cofactor F420in prokaryotes.
Authors: Bashiri, G. / Antoney, J. / Jirgis, E.N.M. / Shah, M.V. / Ney, B. / Copp, J. / Stuteley, S.M. / Sreebhavan, S. / Palmer, B. / Middleditch, M. / Tokuriki, N. / Greening, C. / Scott, C. / ...Authors: Bashiri, G. / Antoney, J. / Jirgis, E.N.M. / Shah, M.V. / Ney, B. / Copp, J. / Stuteley, S.M. / Sreebhavan, S. / Palmer, B. / Middleditch, M. / Tokuriki, N. / Greening, C. / Scott, C. / Baker, E.N. / Jackson, C.J.
History
DepositionDec 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 8, 2020Group: Structure summary / Category: audit_author
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-phospho-L-lactate guanylyltransferase
B: 2-phospho-L-lactate guanylyltransferase
C: 2-phospho-L-lactate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,21912
Polymers70,5693
Non-polymers6509
Water2,882160
1
A: 2-phospho-L-lactate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7404
Polymers23,5231
Non-polymers2173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-phospho-L-lactate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7404
Polymers23,5231
Non-polymers2173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 2-phospho-L-lactate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7404
Polymers23,5231
Non-polymers2173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.170, 110.441, 165.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 2-phospho-L-lactate guanylyltransferase / LP guanylyltransferase


Mass: 23523.043 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: cofC, Rv2983 / Production host: Mycobacterium smegmatis (bacteria)
References: UniProt: P9WP83, 2-phospho-L-lactate guanylyltransferase
#2: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5O6P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 1500, 3% MPD, 0.2 M MgSO4, 0.1 M sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.18→82.95 Å / Num. obs: 32157 / % possible obs: 100 % / Redundancy: 14.7 % / CC1/2: 0.998 / Net I/σ(I): 14.5
Reflection shellResolution: 2.18→2.25 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2724 / CC1/2: 0.376

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BWG

6bwg


Resolution: 2.18→46.89 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.758 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.241 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28101 1501 4.7 %RANDOM
Rwork0.21864 ---
obs0.22168 30620 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.101 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å2-0 Å2
2--1.5 Å20 Å2
3----1.07 Å2
Refinement stepCycle: 1 / Resolution: 2.18→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4385 0 36 160 4581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0144511
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174116
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.6656119
X-RAY DIFFRACTIONr_angle_other_deg0.9481.6429586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1445608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.77919.765213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96715631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9551547
X-RAY DIFFRACTIONr_chiral_restr0.0760.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
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_it4.8814.7822450
X-RAY DIFFRACTIONr_mcbond_other4.8794.782449
X-RAY DIFFRACTIONr_mcangle_it6.9797.1533052
X-RAY DIFFRACTIONr_mcangle_other6.9797.1553053
X-RAY DIFFRACTIONr_scbond_it5.4495.3392059
X-RAY DIFFRACTIONr_scbond_other5.4265.3452039
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8477.8093067
X-RAY DIFFRACTIONr_long_range_B_refined10.2360.9824952
X-RAY DIFFRACTIONr_long_range_B_other10.24160.9754932
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.18→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 117 -
Rwork0.39 2226 -
obs--99.36 %

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