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- PDB-6uw7: The crystal structure of FbiA from Mycobacterium smegmatis, Dehyd... -

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Basic information

Entry
Database: PDB / ID: 6uw7
TitleThe crystal structure of FbiA from Mycobacterium smegmatis, Dehydro-F420-0 bound form
ComponentsPhosphoenolpyruvate transferase
KeywordsBIOSYNTHETIC PROTEIN / Factor 420 / Phosphotransferase / Metalloenzyme
Function / homology
Function and homology information


2-phospho-L-lactate transferase / LPPG:FO 2-phospho-L-lactate transferase activity / magnesium ion binding
Similarity search - Function
CofD-like domain / Phosphoenolpyruvate transferase/2-phospho-L-lactate transferase / 2-phospho-L-lactate transferase CofD / CofD-like domain superfamily / 2-phospho-L-lactate transferase CofD / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-QMD / Phosphoenolpyruvate transferase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.342 Å
AuthorsGrinter, R. / Gillett, D. / Cordero, P.R.F. / Izore, T. / Greening, C.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1178715 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1142699 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1139832 Australia
CitationJournal: mSystems / Year: 2020
Title: Cellular and Structural Basis of Synthesis of the Unique Intermediate Dehydro-F420-0 in Mycobacteria.
Authors: Grinter, R. / Ney, B. / Brammananth, R. / Barlow, C.K. / Cordero, P.R.F. / Gillett, D.L. / Izore, T. / Cryle, M.J. / Harold, L.K. / Cook, G.M. / Taiaroa, G. / Williamson, D.A. / Warden, A.C. ...Authors: Grinter, R. / Ney, B. / Brammananth, R. / Barlow, C.K. / Cordero, P.R.F. / Gillett, D.L. / Izore, T. / Cryle, M.J. / Harold, L.K. / Cook, G.M. / Taiaroa, G. / Williamson, D.A. / Warden, A.C. / Oakeshott, J.G. / Taylor, M.C. / Crellin, P.K. / Jackson, C.J. / Schittenhelm, R.B. / Coppel, R.L. / Greening, C.
History
DepositionNov 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Author supporting evidence / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_audit_support / struct
Item: _struct.title
Revision 1.2Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _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.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Phosphoenolpyruvate transferase
A: Phosphoenolpyruvate transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3597
Polymers69,5812
Non-polymers7785
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-26 kcal/mol
Surface area26120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.120, 73.300, 90.338
Angle α, β, γ (deg.)90.000, 96.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphoenolpyruvate transferase / EPPG:FO PEP transferase


Mass: 34790.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: fbiA, MSMEG_1830, MSMEI_1787
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTG2, 2-phospho-L-lactate transferase
#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: Chemical ChemComp-QMD / 2-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-[2,4,8-tris(oxidanylidene)-1,9-dihydropyrimido[4,5-b]quinolin-10-yl]pentoxy]phosphoryl]oxyprop-2-enoic acid


Mass: 513.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C19H20N3O12P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 43.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 18 % PEG6000, 0.1 M Tris, 0.2 M Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.34→45.843 Å / Num. obs: 25198 / % possible obs: 99.4 % / Redundancy: 7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.054 / Net I/σ(I): 12.2
Reflection shellResolution: 2.34→2.42 Å / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2331 / CC1/2: 0.857 / Rpim(I) all: 0.252

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C3D

3c3d


Resolution: 2.342→45.843 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2203 1218 4.84 %
Rwork0.1629 23959 -
obs0.1656 25177 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.26 Å2 / Biso mean: 29.9576 Å2 / Biso min: 11.01 Å2
Refinement stepCycle: final / Resolution: 2.342→45.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4715 0 83 197 4995
Biso mean--45.37 29.24 -
Num. residues----632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.342-2.43570.27031450.2039251995
2.4357-2.54660.25171410.1792651100
2.5466-2.68080.22531310.182642100
2.6808-2.84880.25851410.1742668100
2.8488-3.06870.27411290.17652688100
3.0687-3.37740.22941270.16142664100
3.3774-3.86590.21861310.1482693100
3.8659-4.86970.1751410.13552687100
4.8697-45.8430.19041320.16972747100
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)
10.9351-0.3603-0.4641.58630.28430.79170.050.1606-0.0622-0.3445-0.0746-0.0261-0.0119-0.0650.01330.23820.0198-0.04350.2023-0.00550.162351.18515.61713.883
20.54290.2916-0.31750.7403-0.42610.97670.04650.04430.04080.07410.04810.1836-0.0934-0.0707-0.08060.15950.00910.00440.15750.01380.207825.52412.90555.063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:326 )B1 - 326
2X-RAY DIFFRACTION2( CHAIN A AND RESID 1:326 )A1 - 326

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