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

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Basic information

Entry
Database: PDB / ID: 5udw
TitleLarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with nickel
ComponentsLactate racemization operon protein LarE
KeywordsTRANSFERASE / Lar / sulfur transferase / LarE / AMPylation / 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
NICKEL (II) ION / 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: 2.698 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 / 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_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.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: 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)192,87337
Polymers190,3136
Non-polymers2,56031
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16770 Å2
ΔGint-410 kcal/mol
Surface area61510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.800, 106.800, 317.266
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 2 through 3 or (resid 4...
21(chain B and (resid 2 through 3 or (resid 4...
31(chain C and (resid 2 through 3 or (resid 4...
41(chain D and (resid 2 through 6 or (resid 7...
51(chain E and (resid 2 through 6 or (resid 7...
61(chain F and (resid 2 through 3 or (resid 4...

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
11ALAALATHRTHR(chain A and (resid 2 through 3 or (resid 4...AA2 - 32 - 3
12LEULEUALAALA(chain A and (resid 2 through 3 or (resid 4...AA4 - 54 - 5
13ALAALAARGARG(chain A and (resid 2 through 3 or (resid 4...AA2 - 2592 - 259
14ALAALAARGARG(chain A and (resid 2 through 3 or (resid 4...AA2 - 2592 - 259
15ALAALAARGARG(chain A and (resid 2 through 3 or (resid 4...AA2 - 2592 - 259
16ALAALAARGARG(chain A and (resid 2 through 3 or (resid 4...AA2 - 2592 - 259
21ALAALATHRTHR(chain B and (resid 2 through 3 or (resid 4...BB2 - 32 - 3
22LEULEUALAALA(chain B and (resid 2 through 3 or (resid 4...BB4 - 54 - 5
23ALAALAARGARG(chain B and (resid 2 through 3 or (resid 4...BB2 - 2592 - 259
24ALAALAARGARG(chain B and (resid 2 through 3 or (resid 4...BB2 - 2592 - 259
25ALAALAARGARG(chain B and (resid 2 through 3 or (resid 4...BB2 - 2592 - 259
26ALAALAARGARG(chain B and (resid 2 through 3 or (resid 4...BB2 - 2592 - 259
31ALAALATHRTHR(chain C and (resid 2 through 3 or (resid 4...CC2 - 32 - 3
32LEULEUALAALA(chain C and (resid 2 through 3 or (resid 4...CC4 - 54 - 5
33ALAALAARGARG(chain C and (resid 2 through 3 or (resid 4...CC2 - 2592 - 259
34ALAALAARGARG(chain C and (resid 2 through 3 or (resid 4...CC2 - 2592 - 259
35ALAALAARGARG(chain C and (resid 2 through 3 or (resid 4...CC2 - 2592 - 259
36ALAALAARGARG(chain C and (resid 2 through 3 or (resid 4...CC2 - 2592 - 259
41ALAALATHRTHR(chain D and (resid 2 through 6 or (resid 7...DD2 - 62 - 6
42LYSLYSALAALA(chain D and (resid 2 through 6 or (resid 7...DD7 - 97 - 9
43ALAALAARGARG(chain D and (resid 2 through 6 or (resid 7...DD2 - 2592 - 259
44ALAALAARGARG(chain D and (resid 2 through 6 or (resid 7...DD2 - 2592 - 259
45ALAALAARGARG(chain D and (resid 2 through 6 or (resid 7...DD2 - 2592 - 259
46ALAALAARGARG(chain D and (resid 2 through 6 or (resid 7...DD2 - 2592 - 259
51ALAALATHRTHR(chain E and (resid 2 through 6 or (resid 7...EE2 - 62 - 6
52LYSLYSALAALA(chain E and (resid 2 through 6 or (resid 7...EE7 - 97 - 9
53ALAALAPHEPHE(chain E and (resid 2 through 6 or (resid 7...EE2 - 2582 - 258
54ALAALAPHEPHE(chain E and (resid 2 through 6 or (resid 7...EE2 - 2582 - 258
55ALAALAPHEPHE(chain E and (resid 2 through 6 or (resid 7...EE2 - 2582 - 258
56ALAALAPHEPHE(chain E and (resid 2 through 6 or (resid 7...EE2 - 2582 - 258
61ALAALATHRTHR(chain F and (resid 2 through 3 or (resid 4...FF2 - 32 - 3
62LEULEUALAALA(chain F and (resid 2 through 3 or (resid 4...FF4 - 54 - 5
63ALAALASERSER(chain F and (resid 2 through 3 or (resid 4...FF2 - 2602 - 260
64ALAALASERSER(chain F and (resid 2 through 3 or (resid 4...FF2 - 2602 - 260
65ALAALASERSER(chain F and (resid 2 through 3 or (resid 4...FF2 - 2602 - 260
66ALAALASERSER(chain F and (resid 2 through 3 or (resid 4...FF2 - 2602 - 260

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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-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 58.693 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.38 Å3/Da / Density % sol: 48.25 % / Mosaicity: 0.11 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3 ul ~24 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 1 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 50 mM ammonium sulfate containing ...Details: 3 ul ~24 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 1 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 50 mM ammonium sulfate containing crushed LarE crystals as microseeds. Sitting drop reservoir contained 100 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 50 mM ammonium sulfate. Crystal soaked 4.5 minutes in 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 5.5, 50 mM ammonium sulfate, 38 mM nickle sulfate.

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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 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.689→48.581 Å / Num. obs: 51502 / % possible obs: 99.8 % / Redundancy: 8.1 % / Biso Wilson estimate: 53.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 20.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.7-2.788.20.8380.788198.5
11.12-48.586.60.0260.999198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.34 Å48.58 Å
Translation8.34 Å48.58 Å

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Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UDQ

5udq


Resolution: 2.698→48.581 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 26.8
RfactorNum. reflection% reflection
Rfree0.2573 4653 4.83 %
Rwork0.1978 --
obs0.2007 48124 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.31 Å2 / Biso mean: 58.5042 Å2 / Biso min: 19.29 Å2
Refinement stepCycle: final / Resolution: 2.698→48.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11010 0 111 100 11221
Biso mean--75.55 47.41 -
Num. residues----1475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911341
X-RAY DIFFRACTIONf_angle_d1.10215375
X-RAY DIFFRACTIONf_chiral_restr0.0671796
X-RAY DIFFRACTIONf_plane_restr0.0071990
X-RAY DIFFRACTIONf_dihedral_angle_d15.0313871
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5528X-RAY DIFFRACTION11.737TORSIONAL
12B5528X-RAY DIFFRACTION11.737TORSIONAL
13C5528X-RAY DIFFRACTION11.737TORSIONAL
14D5528X-RAY DIFFRACTION11.737TORSIONAL
15E5528X-RAY DIFFRACTION11.737TORSIONAL
16F5528X-RAY DIFFRACTION11.737TORSIONAL
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 (%)
2.6982-2.72880.3671300.3022992312296
2.7288-2.76090.37731490.300930033152100
2.7609-2.79460.3331590.290431023261100
2.7946-2.82990.36251450.284230103155100
2.8299-2.86720.3021440.26830853229100
2.8672-2.90650.34131520.262930703222100
2.9065-2.9480.31981520.246230523204100
2.948-2.9920.36551450.262330573202100
2.992-3.03870.31961510.252930753226100
3.0387-3.08850.36951720.262930173189100
3.0885-3.14180.37031540.25431103264100
3.1418-3.19890.3321690.24829993168100
3.1989-3.26040.34251380.24430613199100
3.2604-3.32690.3061550.234130833238100
3.3269-3.39930.2912020.21429673169100
3.3993-3.47830.23691610.205530773238100
3.4783-3.56530.28481570.192530893246100
3.5653-3.66160.28631480.192230363184100
3.6616-3.76940.25421550.182530673222100
3.7694-3.8910.21221720.168830443216100
3.891-4.030.20421620.158930303192100
4.03-4.19120.22281590.148830733232100
4.1912-4.38190.21721560.149330503206100
4.3819-4.61270.17911260.14730993225100
4.6127-4.90150.19881660.158630513217100
4.9015-5.27950.26481520.162530523204100
5.2795-5.810.21671630.19130663229100
5.81-6.64890.25591610.202130573218100
6.6489-8.370.22861470.194130663213100
8.37-48.58880.2081510.19093056320799
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)
11.0988-1.15590.13685.87540.15642.3348-0.2054-0.3403-0.1990.53050.4181-0.130.02860.2274-0.20930.32810.05770.00640.51910.00810.379434.3641-48.9716-18.6706
20.6151-0.89140.33367.03061.29820.4758-0.1363-0.3332-0.39110.63190.34390.97450.0201-0.1039-0.2390.40430.04590.10130.55930.13540.540526.3209-45.7709-17.2464
37.2033-1.0566-0.38275.57410.08985.558-0.07580.3271-0.1272-0.07370.1668-0.1545-0.21610.0393-0.08660.2935-0.01770.00160.2513-0.05490.180834.9578-22.6755-2.7325
43.68770.50250.27414.54264.24276.72850.06130.0138-0.65190.2899-0.18090.21520.42590.10880.11120.2961-0.0204-0.02940.3082-0.00450.487845.9181-54.857122.991
50.7745-0.8062-0.29884.49013.68792.29060.03170.2193-0.3429-0.3893-0.047-0.0267-0.2376-0.17140.02490.4027-0.0795-0.01810.4446-0.03210.495245.3029-48.154516.3714
63.810.2883-0.59157.2411-4.07374.8329-0.0883-0.07940.1503-0.0157-0.0754-0.1076-0.10420.07460.1380.2231-0.03480.00670.2265-0.07640.22335.9554-27.857828.0432
73.7411-4.1608-1.75468.31983.10071.99410.3065-0.00430.1291-0.3639-0.1242-0.1922-0.09-0.1202-0.17320.2716-0.0268-0.04480.3443-0.00070.30036.7873-58.180510.1898
81.5947-4.5853-1.16279.17381.5719-0.1831-0.2568-0.76520.44050.4730.6479-0.8140.03420.2794-0.40180.4328-0.0474-0.10690.7598-0.11610.513511.2352-55.363117.6433
98.91471.91140.67285.69531.6377.57120.20630.06980.1102-0.19930.15860.2592-0.153-0.267-0.34250.22490.0314-0.00130.2320.02280.28368.9759-27.971112.5208
101.7769-1.82130.31864.422.23283.22030.1089-0.14030.0503-1.1523-0.33910.1734-1.454-0.43150.1661.09310.0796-0.19070.4597-0.03410.389539.677716.756932.3397
111.0676-1.8873-1.01525.33732.61152.48630.10710.2079-0.2144-0.8168-0.43060.7427-0.6949-0.52530.24530.6240.0164-0.18220.4795-0.04380.399737.198911.520135.8042
124.52851.3587-1.24174.5802-1.13713.64330.1952-0.11380.444-0.0349-0.1154-0.0715-0.06560.213-0.05030.3297-0.0377-0.02160.2072-0.04010.24541.3126-9.747522.1852
137.73012.7959-1.65665.4873-3.0197.1425-0.1539-0.56790.3340.44150.2204-0.1634-0.30990.0336-0.11180.3664-0.0322-0.02810.1968-0.07310.250341.2032-15.056626.3797
142.52380.85680.056.9988-1.45752.9864-0.5728-0.66230.86671.3940.60980.0935-1.0879-0.1742-0.13851.13820.4453-0.27840.8225-0.11191.12710.649412.886825.6047
152.05590.68570.45517.3879-3.20042.0478-0.6578-0.47870.1980.47780.55820.3816-0.6225-0.63180.11870.6830.1975-0.11110.867-0.04190.7271-1.09537.803321.064
163.89470.84930.41886.4143-0.16788.01180.0326-0.37660.11180.50770.32750.3805-0.7753-0.8356-0.35390.35580.11980.03350.39820.00110.312810.4673-14.663225.3132
171.522-0.2315-0.76575.62412.71043.66390.0240.2746-0.0028-0.6247-0.13670.082-0.0845-0.11580.1140.42980.0359-0.04550.27940.07050.30727.829721.8048-4.8551
186.10410.76820.50047.5168-0.36562.9629-0.1725-0.047-0.5616-0.1114-0.0209-0.61070.87230.45370.21030.42580.063-0.08020.2342-0.03120.387234.097122.04683.9517
195.3033.5917-3.91057.5558-1.51939.077-0.26760.5410.1311-0.89190.22250.1282-0.5503-0.23090.10410.60890.07810.03120.29010.05780.377124.1024-0.972-8.8255
209.12080.06681.97476.1812-0.84415.3574-0.03470.23070.1797-0.25260.0217-0.0147-0.30150.0559-0.00560.38690.01540.01420.18940.0030.203825.1253-9.9036-1.219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 115 )A2 - 115
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 189 )A116 - 189
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 259 )A190 - 259
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 115 )B2 - 115
5X-RAY DIFFRACTION5chain 'B' and (resid 116 through 189 )B116 - 189
6X-RAY DIFFRACTION6chain 'B' and (resid 190 through 259 )B190 - 259
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 115 )C2 - 115
8X-RAY DIFFRACTION8chain 'C' and (resid 116 through 189 )C116 - 189
9X-RAY DIFFRACTION9chain 'C' and (resid 190 through 259 )C190 - 259
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 95 )D2 - 95
11X-RAY DIFFRACTION11chain 'D' and (resid 96 through 189 )D96 - 189
12X-RAY DIFFRACTION12chain 'D' and (resid 190 through 245 )D190 - 245
13X-RAY DIFFRACTION13chain 'D' and (resid 246 through 259 )D246 - 259
14X-RAY DIFFRACTION14chain 'E' and (resid 2 through 95 )E2 - 95
15X-RAY DIFFRACTION15chain 'E' and (resid 96 through 189 )E96 - 189
16X-RAY DIFFRACTION16chain 'E' and (resid 190 through 258 )E190 - 258
17X-RAY DIFFRACTION17chain 'F' and (resid 2 through 115 )F2 - 115
18X-RAY DIFFRACTION18chain 'F' and (resid 116 through 177 )F116 - 177
19X-RAY DIFFRACTION19chain 'F' and (resid 178 through 206 )F178 - 206
20X-RAY DIFFRACTION20chain 'F' and (resid 207 through 260 )F207 - 260

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