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- PDB-5uds: LarE, a sulfur transferase involved in synthesis of the cofactor ... -

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Basic information

Entry
Database: PDB / ID: 5uds
TitleLarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with MgATP
ComponentsLactate racemization operon protein LarE
KeywordsTRANSFERASE / Lar / sulfur transferase / LarE / AMPylation / hexamer / trimer / PP-loop / ATP / magnesium / 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
ADENOSINE-5'-TRIPHOSPHATE / 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: 2.37 Å
AuthorsFellner, M. / Desguin, B. / Hausinger, R.P. / Hu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1516126 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE.
Authors: Fellner, M. / Desguin, B. / Hausinger, R.P. / Hu, J.
History
DepositionDec 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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 / diffrn_radiation_wavelength / 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.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactate racemization operon protein LarE
B: Lactate racemization operon protein LarE
C: Lactate racemization operon protein LarE
D: Lactate racemization operon protein LarE
E: Lactate racemization operon protein LarE
F: Lactate racemization operon protein LarE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,07124
Polymers190,3136
Non-polymers3,75918
Water18,6091033
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19990 Å2
ΔGint-169 kcal/mol
Surface area61090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.724, 107.724, 318.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11C-722-

HOH

21E-714-

HOH

31E-756-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESID 3 THROUGH 6 OR (RESID 7...
211(CHAIN B AND (RESID 3 THROUGH 6 OR (RESID 7...
311(CHAIN C AND (RESID 3 THROUGH 6 OR (RESID 7...
411(CHAIN D AND (RESID 3 THROUGH 18 OR (RESID 20...
511(CHAIN E AND (RESID 3 THROUGH 6 OR (RESID 7...
611(CHAIN F AND (RESID 3 THROUGH 6 OR (RESID 7...

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Lactate racemization operon protein LarE


Mass: 31718.766 Da / Num. of mol.: 6
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
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1033 / 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: 2.42 Å3/Da / Density % sol: 49.26 % / Mosaicity: 0.23 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4 ul ~39 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 4 ul reservoir solution. Hanging drop reservoir contained 100 ul of 27.5% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 ...Details: 4 ul ~39 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 4 ul reservoir solution. Hanging drop reservoir contained 100 ul of 27.5% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 105 mM ammonium sulfate). Crystal soaked 3 minutes in 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 50 mM ammonium sulfate, 18.5 mM adenosine triphosphate, 40 mM magnesium chloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.367→48.02 Å / Num. obs: 77278 / % possible obs: 99.8 % / Redundancy: 9.9 % / Biso Wilson estimate: 36.77 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 19.1
Reflection shellResolution: 2.37→2.42 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.965 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.35 Å48.02 Å
Translation8.35 Å48.02 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UDQ

5udq


Resolution: 2.37→47.63 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 24.7
RfactorNum. reflection% reflection
Rfree0.257 7312 5.03 %
Rwork0.191 --
obs0.195 72732 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.45 Å2
Refinement stepCycle: LAST / Resolution: 2.37→47.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11553 0 222 1033 12808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711992
X-RAY DIFFRACTIONf_angle_d0.97616310
X-RAY DIFFRACTIONf_dihedral_angle_d3.5948316
X-RAY DIFFRACTIONf_chiral_restr0.0541893
X-RAY DIFFRACTIONf_plane_restr0.0062076
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A6306X-RAY DIFFRACTIONPOSITIONAL
12B6306X-RAY DIFFRACTIONPOSITIONAL
13C6306X-RAY DIFFRACTIONPOSITIONAL
14D6306X-RAY DIFFRACTIONPOSITIONAL
15E6306X-RAY DIFFRACTIONPOSITIONAL
16F6306X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3672-2.39410.35552420.2814389X-RAY DIFFRACTION95
2.3941-2.42230.30862730.26734552X-RAY DIFFRACTION100
2.4223-2.45180.32092580.25134663X-RAY DIFFRACTION100
2.4518-2.48290.33682290.25574602X-RAY DIFFRACTION100
2.4829-2.51550.29892810.24664545X-RAY DIFFRACTION100
2.5155-2.550.32052320.2394632X-RAY DIFFRACTION100
2.55-2.58640.30772540.24074617X-RAY DIFFRACTION100
2.5864-2.6250.32462670.23764644X-RAY DIFFRACTION100
2.625-2.66610.33032570.24024556X-RAY DIFFRACTION100
2.6661-2.70980.30962260.22594622X-RAY DIFFRACTION100
2.7098-2.75650.33742780.22244582X-RAY DIFFRACTION100
2.7565-2.80660.30622990.21884545X-RAY DIFFRACTION100
2.8066-2.86060.32042120.21764649X-RAY DIFFRACTION100
2.8606-2.9190.31412120.20984674X-RAY DIFFRACTION100
2.919-2.98240.28812570.21544589X-RAY DIFFRACTION100
2.9824-3.05180.32022180.22244628X-RAY DIFFRACTION100
3.0518-3.12810.30582320.20724618X-RAY DIFFRACTION100
3.1281-3.21260.29862030.20284671X-RAY DIFFRACTION100
3.2126-3.30720.27532410.18914606X-RAY DIFFRACTION100
3.3072-3.41390.262620.18934578X-RAY DIFFRACTION100
3.4139-3.53580.25573070.18564551X-RAY DIFFRACTION100
3.5358-3.67740.23341850.17744651X-RAY DIFFRACTION100
3.6774-3.84470.22962000.1664706X-RAY DIFFRACTION100
3.8447-4.04730.2122100.15834623X-RAY DIFFRACTION100
4.0473-4.30070.22432590.16284610X-RAY DIFFRACTION100
4.3007-4.63250.21162050.16284649X-RAY DIFFRACTION100
4.6325-5.09820.22192760.15764590X-RAY DIFFRACTION100
5.0982-5.83480.24072520.17574575X-RAY DIFFRACTION100
5.8348-7.34690.212430.17994620X-RAY DIFFRACTION100
7.3469-47.64190.17542420.174616X-RAY DIFFRACTION100

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