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

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Basic information

Entry
Database: PDB / ID: 6utp
TitleLarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with cobalt
ComponentsATP-dependent sacrificial sulfur transferase LarE
KeywordsTRANSFERASE / Lar / sulfur transferase / AMPylation / PP-loop / ATP pyrophophatase domain / lactate racemization / lactate racemase
Function / homology
Function and homology information


pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase / NAD+ synthase (glutamine-hydrolysing) / sulfurtransferase activity / NAD+ synthase (glutamine-hydrolyzing) 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 / ATP-dependent sacrificial sulfur transferase LarE / Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.55 Å
AuthorsFellner, M. / Huizenga, K. / Hausinger, R.P. / Hu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1516126 United States
CitationJournal: Sci Rep / Year: 2020
Title: Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE.
Authors: Fellner, M. / Huizenga, K.G. / Hausinger, R.P. / Hu, J.
History
DepositionOct 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 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 1.4Oct 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_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.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.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.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_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: ATP-dependent sacrificial sulfur transferase LarE
B: ATP-dependent sacrificial sulfur transferase LarE
C: ATP-dependent sacrificial sulfur transferase LarE
D: ATP-dependent sacrificial sulfur transferase LarE
E: ATP-dependent sacrificial sulfur transferase LarE
F: ATP-dependent sacrificial sulfur transferase LarE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,19728
Polymers190,3136
Non-polymers1,88422
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Hexamer on gel filtration.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15670 Å2
ΔGint-316 kcal/mol
Surface area59990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.210, 106.210, 313.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 10 through 11 and (name N...
21(chain B and ((resid 10 through 11 and (name N...
31(chain C and ((resid 10 through 11 and (name N...
41(chain D and ((resid 10 through 11 and (name N...
51(chain E and (resid 10 through 25 or (resid 26...
61(chain F and ((resid 10 through 11 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
11THRTHRLEULEU(chain A and ((resid 10 through 11 and (name N...AA10 - 1110 - 11
12THRTHRPHEPHE(chain A and ((resid 10 through 11 and (name N...AA3 - 2583 - 258
13THRTHRPHEPHE(chain A and ((resid 10 through 11 and (name N...AA3 - 2583 - 258
21THRTHRLEULEU(chain B and ((resid 10 through 11 and (name N...BB10 - 1110 - 11
22ALAALAARGARG(chain B and ((resid 10 through 11 and (name N...BB2 - 2592 - 259
23ALAALAARGARG(chain B and ((resid 10 through 11 and (name N...BB2 - 2592 - 259
31THRTHRLEULEU(chain C and ((resid 10 through 11 and (name N...CC10 - 1110 - 11
32ALAALAARGARG(chain C and ((resid 10 through 11 and (name N...CC2 - 2592 - 259
33ALAALAARGARG(chain C and ((resid 10 through 11 and (name N...CC2 - 2592 - 259
34ALAALAARGARG(chain C and ((resid 10 through 11 and (name N...CC2 - 2592 - 259
35ALAALAARGARG(chain C and ((resid 10 through 11 and (name N...CC2 - 2592 - 259
41THRTHRLEULEU(chain D and ((resid 10 through 11 and (name N...DD10 - 1110 - 11
42THRTHRARGARG(chain D and ((resid 10 through 11 and (name N...DD3 - 2593 - 259
43THRTHRARGARG(chain D and ((resid 10 through 11 and (name N...DD3 - 2593 - 259
44THRTHRARGARG(chain D and ((resid 10 through 11 and (name N...DD3 - 2593 - 259
45THRTHRARGARG(chain D and ((resid 10 through 11 and (name N...DD3 - 2593 - 259
51THRTHRPHEPHE(chain E and (resid 10 through 25 or (resid 26...EE10 - 2510 - 25
52SERSERSERSER(chain E and (resid 10 through 25 or (resid 26...EE2626
53THRTHRPHEPHE(chain E and (resid 10 through 25 or (resid 26...EE10 - 25810 - 258
54THRTHRPHEPHE(chain E and (resid 10 through 25 or (resid 26...EE10 - 25810 - 258
55THRTHRPHEPHE(chain E and (resid 10 through 25 or (resid 26...EE10 - 25810 - 258
56THRTHRPHEPHE(chain E and (resid 10 through 25 or (resid 26...EE10 - 25810 - 258
61THRTHRLEULEU(chain F and ((resid 10 through 11 and (name N...FF10 - 1110 - 11
62ALAALASERSER(chain F and ((resid 10 through 11 and (name N...FF2 - 2602 - 260
63ALAALASERSER(chain F and ((resid 10 through 11 and (name N...FF2 - 2602 - 260
64ALAALASERSER(chain F and ((resid 10 through 11 and (name N...FF2 - 2602 - 260
65ALAALASERSER(chain F and ((resid 10 through 11 and (name N...FF2 - 2602 - 260

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Components

#1: Protein
ATP-dependent sacrificial sulfur transferase LarE / ATP-utilizing enzyme of the PP-loopsuperfamily / Lactate racemization operon protein LarE / PP-loop ...ATP-utilizing enzyme of the PP-loopsuperfamily / Lactate racemization operon protein LarE / PP-loop superfamily ATP-binding protein / TIGR00268 family protein


Mass: 31718.766 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria)
Gene: larE, AVR82_02840, BIZ32_00440, CFM86_00460, CUR48_11145, E3O64_03880, IV39_GL000116, LPJSA22_00116, LpLQ80_00490, Nizo1839_0768, Nizo2891_3302
Plasmid: pGIR076 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic express DE3 / References: UniProt: A0A0G9FES3, UniProt: F9UST4*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.32 Å3/Da / Density % sol: 47.05 % / Mosaicity: 0.97 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.6 uL ~24 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 1.2 uL of reservoir solution. Hanging drop reservoir contained 100 uL of 25% v/v pentaerythritol ethoxylate (15/4 EO/OH) ...Details: 0.6 uL ~24 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 1.2 uL of reservoir solution. Hanging drop reservoir contained 100 uL of 25% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM MOPS pH 7.0, 100 mM ammonium sulfate. Crystal soaked 5 minutes in ~20 mM cobalt sulfate, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 50 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.6 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 3.55→87.93 Å / Num. obs: 20329 / % possible obs: 89.6 % / Redundancy: 10.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.068 / Rrim(I) all: 0.237 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.55-3.8311.40.8434382738380.9140.2430.8793.284.4
9.39-87.93120.0541689414080.9980.0160.05621.899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.51 Å87.93 Å
Translation7.51 Å87.93 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.8.3phasing
PHENIX1.17.1-3644refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UDQ

5udq


Resolution: 3.55→87.93 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 29.73
RfactorNum. reflection% reflection
Rfree0.2978 1895 5.23 %
Rwork0.2305 --
obs0.234 20246 87.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.06 Å2 / Biso mean: 74.6558 Å2 / Biso min: 49.78 Å2
Refinement stepCycle: final / Resolution: 3.55→87.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10791 0 86 13 10890
Biso mean--69.81 65.86 -
Num. residues----1451
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3972X-RAY DIFFRACTION4.163TORSIONAL
12B3972X-RAY DIFFRACTION4.163TORSIONAL
13C3972X-RAY DIFFRACTION4.163TORSIONAL
14D3972X-RAY DIFFRACTION4.163TORSIONAL
15E3972X-RAY DIFFRACTION4.163TORSIONAL
16F3972X-RAY DIFFRACTION4.163TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.55-3.640.31121270.28262341246883
3.64-3.740.32881390.28692270240982
3.74-3.850.31691220.2532332245482
3.85-3.970.23071240.23842327245183
3.97-4.110.311350.24172345248084
4.11-4.280.3281150.23712349246483
4.28-4.470.30811310.22182371250284
4.47-4.710.29641330.22122341247484
4.71-50.30341320.22362390252285
5-5.390.31131410.2372494263588
5.39-5.930.33131260.25562535266190
5.93-6.790.31951510.25942645279695
6.79-8.550.28811840.211427602944100
8.55-87.930.25381350.186328282963100

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