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- PDB-6uvx: The crystal structure of FbiA from Mycobacterium Smegmatis, Apo state -

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Basic information

Entry
Database: PDB / ID: 6uvx
TitleThe crystal structure of FbiA from Mycobacterium Smegmatis, Apo state
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
Phosphoenolpyruvate transferase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGrinter, R. / Gillett, D. / Cordero, P.R.F. / 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 ...audit_author / citation / citation_author / pdbx_audit_support
Item: _audit_author.name / _citation.journal_id_ISSN
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 / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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 / _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
B: Phosphoenolpyruvate transferase
A: Phosphoenolpyruvate transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7015
Polymers69,5812
Non-polymers1203
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-27 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.082, 73.789, 91.466
Angle α, β, γ (deg.)90.000, 94.980, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 247 or resid 250 through 326))
21(chain B and (resid 1 through 93 or resid 98 through 326))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPROPRO(chain A and (resid 1 through 247 or resid 250 through 326))AB1 - 2471 - 247
12GLYGLYSERSER(chain A and (resid 1 through 247 or resid 250 through 326))AB250 - 326250 - 326
21METMETVALVAL(chain B and (resid 1 through 93 or resid 98 through 326))BA1 - 931 - 93
22PHEPHESERSER(chain B and (resid 1 through 93 or resid 98 through 326))BA98 - 32698 - 326

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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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 17% PEG 3350, 0.2 M Calcium Acetate, 0.1 M Tris, 20 % Glycerol

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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: Sep 11, 2019 / Details: Silicon
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→45.91 Å / Num. obs: 27208 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.982 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.149 / Net I/σ(I): 6.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2626 / CC1/2: 0.523 / Rpim(I) all: 0.841 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C3D

3c3d


Resolution: 2.3→45.907 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 1369 5.04 %
Rwork0.1932 25791 -
obs0.1965 27160 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.43 Å2 / Biso mean: 39.0111 Å2 / Biso min: 10.58 Å2
Refinement stepCycle: final / Resolution: 2.3→45.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 3 103 4916
Biso mean--36.08 29.61 -
Num. residues----645
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1938X-RAY DIFFRACTION10.481TORSIONAL
12B1938X-RAY DIFFRACTION10.481TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3002-2.38240.31541390.255251199
2.3824-2.47780.27861420.2422548100
2.4778-2.59050.33741340.2451255899
2.5905-2.72710.3351480.23482606100
2.7271-2.89790.30181430.22672553100
2.8979-3.12160.30671330.22362584100
3.1216-3.43570.24911380.20392563100
3.4357-3.93260.27041320.17152607100
3.9326-4.95370.20251560.14712585100
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)
11.32470.1214-0.75851.5847-0.05610.96860.00410.3742-0.1408-0.4892-0.0097-0.17490.0469-0.1530.00280.31370.01640.00390.2887-0.06660.236152.102515.822414.1152
20.66180.1688-0.30921.2862-0.78221.20790.05390.04780.00660.13920.0880.3011-0.1206-0.1233-0.10670.17380.00590.00360.1469-0.00130.214526.337412.575655.2325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resseq 1:326)B1 - 326
2X-RAY DIFFRACTION2(chain A and resseq 1:326)A1 - 326

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