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- PDB-6dg3: LarE, a sulfur transferase involved in synthesis of the cofactor ... -

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Basic information

Entry
Database: PDB / ID: 6dg3
TitleLarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with caesium
ComponentsPyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
KeywordsTRANSFERASE / Lar / sulfur transferase / LarE / AMPylation / caesium / hexamer / trimer / PP-loop / ATP pyrophophatase domain / lactate / lactate racemization / lactate racemase
Function / homology
Function and homology information


pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase / sulfurtransferase activity / lyase activity / ATP binding
Similarity search - Function
Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase LarE / NAD/GMP synthase / NAD synthase / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
: / PHOSPHATE ION / Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.944 Å
AuthorsFellner, M. / Hausinger, R.P. / Hu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1516126 United States
CitationJournal: J Life Sci / Year: 2021
Title: Unique cesium-binding sites in proteins, a case study with the sacrificial sulfur transferase LarE
Authors: Fellner, M.
History
DepositionMay 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 12, 2021Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _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.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
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _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: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
B: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
C: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
E: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
G: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
H: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
I: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
J: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
K: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
L: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)383,36036
Polymers380,62512
Non-polymers2,73524
Water1267
1
A: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
E: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
J: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
L: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
hetero molecules

I: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
K: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,68018
Polymers190,3136
Non-polymers1,36712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x+1/2,y+1/2,z1
2
B: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
C: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
D: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
F: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
G: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
H: Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,68018
Polymers190,3136
Non-polymers1,36712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.371, 154.161, 328.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 8 through 21 and (name N...
21(chain C and ((resid 8 through 21 and (name N...
31(chain D and ((resid 8 through 21 and (name N...
41(chain E and ((resid 8 through 21 and (name N...
51(chain F and ((resid 8 through 21 and (name N...
61(chain G and ((resid 8 through 21 and (name N...
71(chain H and ((resid 8 through 21 and (name N...
81(chain I and ((resid 8 through 21 and (name N...
91(chain J and ((resid 8 through 21 and (name N...
101(chain K and ((resid 8 through 21 and (name N...
111(chain L and ((resid 8 through 21 and (name N...

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
11LYSLYSVALVAL(chain A and ((resid 8 through 21 and (name N...AA8 - 218 - 21
12THRTHRPHEPHE(chain A and ((resid 8 through 21 and (name N...AA3 - 2583 - 258
13THRTHRPHEPHE(chain A and ((resid 8 through 21 and (name N...AA3 - 2583 - 258
14THRTHRPHEPHE(chain A and ((resid 8 through 21 and (name N...AA3 - 2583 - 258
15THRTHRPHEPHE(chain A and ((resid 8 through 21 and (name N...AA3 - 2583 - 258
21LYSLYSVALVAL(chain C and ((resid 8 through 21 and (name N...CC8 - 218 - 21
22THRTHRPHEPHE(chain C and ((resid 8 through 21 and (name N...CC3 - 2583 - 258
23THRTHRPHEPHE(chain C and ((resid 8 through 21 and (name N...CC3 - 2583 - 258
24THRTHRPHEPHE(chain C and ((resid 8 through 21 and (name N...CC3 - 2583 - 258
25THRTHRPHEPHE(chain C and ((resid 8 through 21 and (name N...CC3 - 2583 - 258
31LYSLYSVALVAL(chain D and ((resid 8 through 21 and (name N...DD8 - 218 - 21
32THRTHRPHEPHE(chain D and ((resid 8 through 21 and (name N...DD3 - 2583 - 258
33THRTHRPHEPHE(chain D and ((resid 8 through 21 and (name N...DD3 - 2583 - 258
34THRTHRPHEPHE(chain D and ((resid 8 through 21 and (name N...DD3 - 2583 - 258
35THRTHRPHEPHE(chain D and ((resid 8 through 21 and (name N...DD3 - 2583 - 258
41LYSLYSVALVAL(chain E and ((resid 8 through 21 and (name N...EE8 - 218 - 21
42LYSLYSPHEPHE(chain E and ((resid 8 through 21 and (name N...EE8 - 2588 - 258
43LYSLYSPHEPHE(chain E and ((resid 8 through 21 and (name N...EE8 - 2588 - 258
44LYSLYSPHEPHE(chain E and ((resid 8 through 21 and (name N...EE8 - 2588 - 258
45LYSLYSPHEPHE(chain E and ((resid 8 through 21 and (name N...EE8 - 2588 - 258
51LYSLYSVALVAL(chain F and ((resid 8 through 21 and (name N...FF8 - 218 - 21
52ALAALAARGARG(chain F and ((resid 8 through 21 and (name N...FF2 - 2592 - 259
53ALAALAARGARG(chain F and ((resid 8 through 21 and (name N...FF2 - 2592 - 259
54ALAALAARGARG(chain F and ((resid 8 through 21 and (name N...FF2 - 2592 - 259
55ALAALAARGARG(chain F and ((resid 8 through 21 and (name N...FF2 - 2592 - 259
61LYSLYSVALVAL(chain G and ((resid 8 through 21 and (name N...GG8 - 218 - 21
62THRTHRPHEPHE(chain G and ((resid 8 through 21 and (name N...GG3 - 2583 - 258
63THRTHRPHEPHE(chain G and ((resid 8 through 21 and (name N...GG3 - 2583 - 258
64THRTHRPHEPHE(chain G and ((resid 8 through 21 and (name N...GG3 - 2583 - 258
65THRTHRPHEPHE(chain G and ((resid 8 through 21 and (name N...GG3 - 2583 - 258
71LYSLYSVALVAL(chain H and ((resid 8 through 21 and (name N...HH8 - 218 - 21
72THRTHRPHEPHE(chain H and ((resid 8 through 21 and (name N...HH3 - 2583 - 258
73THRTHRPHEPHE(chain H and ((resid 8 through 21 and (name N...HH3 - 2583 - 258
74THRTHRPHEPHE(chain H and ((resid 8 through 21 and (name N...HH3 - 2583 - 258
75THRTHRPHEPHE(chain H and ((resid 8 through 21 and (name N...HH3 - 2583 - 258
81LYSLYSVALVAL(chain I and ((resid 8 through 21 and (name N...II8 - 218 - 21
82THRTHRPHEPHE(chain I and ((resid 8 through 21 and (name N...II3 - 2583 - 258
83THRTHRPHEPHE(chain I and ((resid 8 through 21 and (name N...II3 - 2583 - 258
84THRTHRPHEPHE(chain I and ((resid 8 through 21 and (name N...II3 - 2583 - 258
85THRTHRPHEPHE(chain I and ((resid 8 through 21 and (name N...II3 - 2583 - 258
91LYSLYSVALVAL(chain J and ((resid 8 through 21 and (name N...JJ8 - 218 - 21
92ALAALASERSER(chain J and ((resid 8 through 21 and (name N...JJ2 - 2602 - 260
93ALAALASERSER(chain J and ((resid 8 through 21 and (name N...JJ2 - 2602 - 260
94ALAALASERSER(chain J and ((resid 8 through 21 and (name N...JJ2 - 2602 - 260
95ALAALASERSER(chain J and ((resid 8 through 21 and (name N...JJ2 - 2602 - 260
101LYSLYSVALVAL(chain K and ((resid 8 through 21 and (name N...KK8 - 218 - 21
102THRTHRPHEPHE(chain K and ((resid 8 through 21 and (name N...KK3 - 2583 - 258
103THRTHRPHEPHE(chain K and ((resid 8 through 21 and (name N...KK3 - 2583 - 258
104THRTHRPHEPHE(chain K and ((resid 8 through 21 and (name N...KK3 - 2583 - 258
105THRTHRPHEPHE(chain K and ((resid 8 through 21 and (name N...KK3 - 2583 - 258
111LYSLYSVALVAL(chain L and ((resid 8 through 21 and (name N...LL8 - 218 - 21
112THRTHRPHEPHE(chain L and ((resid 8 through 21 and (name N...LL3 - 2583 - 258
113THRTHRPHEPHE(chain L and ((resid 8 through 21 and (name N...LL3 - 2583 - 258
114THRTHRPHEPHE(chain L and ((resid 8 through 21 and (name N...LL3 - 2583 - 258
115THRTHRPHEPHE(chain L and ((resid 8 through 21 and (name N...LL3 - 2583 - 258

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Components

#1: Protein
Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase / P2CMN sulfurtransferase / Lactate racemase accessory protein LarE / Lactate racemase activation ...P2CMN sulfurtransferase / Lactate racemase accessory protein LarE / Lactate racemase activation protein LarE / Lactate racemase maturation protein LarE / Lactate racemization operon protein LarE / Nickel-pincer cofactor biosynthesis protein LarE


Mass: 31718.766 Da / Num. of mol.: 12 / Fragment: LarE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1) (bacteria)
Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: larE, lp_0109 / Plasmid: pGIR076 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic express DE3
References: UniProt: F9UST4, Transferases; Transferring sulfur-containing groups; Sulfurtransferases
#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cs
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE INDICATED THAT THIS SEGMENT REPRESENTS A C-TERMINAL FUSION TAG

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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: 2.54 Å3/Da / Density % sol: 51.52 % / Mosaicity: 0.16 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5 ul ~27 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 1 ul 1 M cesium chloride and 4 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 30% v/v ...Details: 5 ul ~27 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 1 ul 1 M cesium chloride and 4 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 30% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 100 mM ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.94→48.91 Å / Num. obs: 81489 / % possible obs: 99.3 % / Redundancy: 6.2 % / Biso Wilson estimate: 48.62 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.049 / Rrim(I) all: 0.123 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.94-360.4742320.8760.2050.51495
15.3-48.914.40.046270.9970.0210.04595.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation9.08 Å48.91 Å
Translation9.08 Å48.91 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.27data scaling
PHASER2.6.0phasing
PHENIXdev-3092refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UDQ

5udq


Resolution: 2.944→48.91 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 27.38
RfactorNum. reflection% reflection
Rfree0.2743 7771 5.06 %
Rwork0.1962 --
obs0.2002 76777 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.92 Å2 / Biso mean: 43.8276 Å2 / Biso min: 9.72 Å2
Refinement stepCycle: final / Resolution: 2.944→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21658 0 72 7 21737
Biso mean--49.54 35 -
Num. residues----2874
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9997X-RAY DIFFRACTION14.607TORSIONAL
12C9997X-RAY DIFFRACTION14.607TORSIONAL
13D9997X-RAY DIFFRACTION14.607TORSIONAL
14E9997X-RAY DIFFRACTION14.607TORSIONAL
15F9997X-RAY DIFFRACTION14.607TORSIONAL
16G9997X-RAY DIFFRACTION14.607TORSIONAL
17H9997X-RAY DIFFRACTION14.607TORSIONAL
18I9997X-RAY DIFFRACTION14.607TORSIONAL
19J9997X-RAY DIFFRACTION14.607TORSIONAL
110K9997X-RAY DIFFRACTION14.607TORSIONAL
111L9997X-RAY DIFFRACTION14.607TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9437-2.97710.38381990.31534503470289
2.9771-3.01210.44792760.295250585334100
3.0121-3.04890.33142460.267749575203100
3.0489-3.08750.312620.22650415303100
3.0875-3.12810.26722750.219849835258100
3.1281-3.17090.32342560.23635010526699
3.1709-3.21620.31032550.24334962521799
3.2162-3.26420.32612290.22755041527099
3.2642-3.31520.31292430.23094949519299
3.3152-3.36950.3082600.22364968522899
3.3695-3.42760.31412480.24054976522499
3.4276-3.48990.33092620.22574956521898
3.4899-3.5570.28552620.21374893515598
3.557-3.62960.34362510.2414977522899
3.6296-3.70850.40822630.28194667493093
3.7085-3.79480.33442970.23934802509997
3.7948-3.88960.27273320.18334858519097
3.8896-3.99470.26773020.17324790509297
3.9947-4.11220.24832330.17064809504296
4.1122-4.24490.24662520.15664758501095
4.2449-4.39650.26642810.1534765504695
4.3965-4.57240.21342620.1494708497094
4.5724-4.78040.26022390.15634737497694
4.7804-5.03210.20192450.14764722496794
5.0321-5.34710.20923010.15454693499495
5.3471-5.75930.20122140.16564819503395
5.7593-6.33780.27032440.1874863510796
6.3378-7.25230.28292550.18994859511497
7.2523-9.12750.19982900.15344812510296
9.1275-48.91740.21992370.18844848508596

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