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- PDB-6bwg: Crystal structure of native Rv2983 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6bwg
TitleCrystal structure of native Rv2983 from Mycobacterium tuberculosis
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 guanylyltransferase
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 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 1.4Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)70,2883
Polymers70,2883
Non-polymers00
Water9,368520
1
A: 2-phospho-L-lactate guanylyltransferase


Theoretical massNumber of molelcules
Total (without water)23,4291
Polymers23,4291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-phospho-L-lactate guanylyltransferase


Theoretical massNumber of molelcules
Total (without water)23,4291
Polymers23,4291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 2-phospho-L-lactate guanylyltransferase


Theoretical massNumber of molelcules
Total (without water)23,4291
Polymers23,4291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.546, 109.058, 166.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-424-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA8 - 21022 - 224
21GLYGLYBB8 - 21022 - 224
12ASPASPAA7 - 21021 - 224
22ASPASPCC7 - 21021 - 224
13GLYGLYBB8 - 21222 - 226
23GLYGLYCC8 - 21222 - 226

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 23429.252 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.14 Å3/Da / Density % sol: 42.65 %
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: 1.99→46.92 Å / Num. obs: 41955 / % possible obs: 99.85 % / Redundancy: 14.8 % / CC1/2: 0.994 / Net I/σ(I): 8.8
Reflection shellResolution: 1.99→2.04 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 1.99→46.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.593 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23448 2149 5.1 %RANDOM
Rwork0.19186 ---
obs0.19408 39762 99.8 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.494 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å2-0 Å2-0 Å2
2--1.16 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 1.99→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4393 0 0 520 4913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0144456
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174121
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.6536094
X-RAY DIFFRACTIONr_angle_other_deg0.8261.6329606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7755611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.50419.72214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27715645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.121548
X-RAY DIFFRACTIONr_chiral_restr0.0480.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02727
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_it4.1192.4572456
X-RAY DIFFRACTIONr_mcbond_other4.1192.4562455
X-RAY DIFFRACTIONr_mcangle_it5.3493.673063
X-RAY DIFFRACTIONr_mcangle_other5.3483.6713064
X-RAY DIFFRACTIONr_scbond_it5.8383.0282000
X-RAY DIFFRACTIONr_scbond_other5.8373.0292001
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5694.3253032
X-RAY DIFFRACTIONr_long_range_B_refined9.02332.3395042
X-RAY DIFFRACTIONr_long_range_B_other8.68631.8644895
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A57570.1
12B57570.1
21A58300.11
22C58300.11
31B59150.09
32C59150.09
LS refinement shellResolution: 1.989→2.041 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 138 -
Rwork0.304 2815 -
obs--97.49 %

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