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

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Open data


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Basic information

Entry
Database: PDB / ID: 5udx
TitleLarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with zinc
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
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: 2.784 Å
AuthorsFellner, M. / Desguin, B. / Hausinger, R.P. / Hu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) 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_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: 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)192,23628
Polymers190,3136
Non-polymers1,92322
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15510 Å2
ΔGint-443 kcal/mol
Surface area62330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.828, 107.828, 319.784
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 14 or (resid 15...
21(chain B and ((resid 2 through 5 and (name N...
31(chain C and ((resid 2 through 5 and (name N...
41(chain D and ((resid 2 through 5 and (name N...
51(chain E and ((resid 2 through 5 and (name N...
61(chain F and ((resid 2 through 5 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
11ALAALAALAALA(chain A and (resid 2 through 14 or (resid 15...AA2 - 142 - 14
12LEULEULYSLYS(chain A and (resid 2 through 14 or (resid 15...AA15 - 1615 - 16
13ALAALAARGARG(chain A and (resid 2 through 14 or (resid 15...AA2 - 2592 - 259
14ALAALAARGARG(chain A and (resid 2 through 14 or (resid 15...AA2 - 2592 - 259
15ALAALAARGARG(chain A and (resid 2 through 14 or (resid 15...AA2 - 2592 - 259
16ALAALAARGARG(chain A and (resid 2 through 14 or (resid 15...AA2 - 2592 - 259
21ALAALAALAALA(chain B and ((resid 2 through 5 and (name N...BB2 - 52 - 5
22ALAALAARGARG(chain B and ((resid 2 through 5 and (name N...BB2 - 2592 - 259
23ALAALAARGARG(chain B and ((resid 2 through 5 and (name N...BB2 - 2592 - 259
24ALAALAARGARG(chain B and ((resid 2 through 5 and (name N...BB2 - 2592 - 259
25ALAALAARGARG(chain B and ((resid 2 through 5 and (name N...BB2 - 2592 - 259
31ALAALAALAALA(chain C and ((resid 2 through 5 and (name N...CC2 - 52 - 5
32ALAALAARGARG(chain C and ((resid 2 through 5 and (name N...CC2 - 2592 - 259
33ALAALAARGARG(chain C and ((resid 2 through 5 and (name N...CC2 - 2592 - 259
34ALAALAARGARG(chain C and ((resid 2 through 5 and (name N...CC2 - 2592 - 259
35ALAALAARGARG(chain C and ((resid 2 through 5 and (name N...CC2 - 2592 - 259
41ALAALAALAALA(chain D and ((resid 2 through 5 and (name N...DD2 - 52 - 5
42ALAALAARGARG(chain D and ((resid 2 through 5 and (name N...DD2 - 2592 - 259
43ALAALAARGARG(chain D and ((resid 2 through 5 and (name N...DD2 - 2592 - 259
44ALAALAARGARG(chain D and ((resid 2 through 5 and (name N...DD2 - 2592 - 259
45ALAALAARGARG(chain D and ((resid 2 through 5 and (name N...DD2 - 2592 - 259
51ALAALAALAALA(chain E and ((resid 2 through 5 and (name N...EE2 - 52 - 5
52ALAALAARGARG(chain E and ((resid 2 through 5 and (name N...EE2 - 2592 - 259
53ALAALAARGARG(chain E and ((resid 2 through 5 and (name N...EE2 - 2592 - 259
54ALAALAARGARG(chain E and ((resid 2 through 5 and (name N...EE2 - 2592 - 259
55ALAALAARGARG(chain E and ((resid 2 through 5 and (name N...EE2 - 2592 - 259
61ALAALAALAALA(chain F and ((resid 2 through 5 and (name N...FF2 - 52 - 5
62ALAALASERSER(chain F and ((resid 2 through 5 and (name N...FF2 - 2602 - 260
63ALAALASERSER(chain F and ((resid 2 through 5 and (name N...FF2 - 2602 - 260
64ALAALASERSER(chain F and ((resid 2 through 5 and (name N...FF2 - 2602 - 260
65ALAALASERSER(chain F and ((resid 2 through 5 and (name N...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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.44 Å3/Da / Density % sol: 49.63 % / Mosaicity: 0.22 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5 ul ~24 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 25.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), ...Details: 5 ul ~24 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 25.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 50 mM ammonium phosphate. 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 zinc sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.78→49 Å / Num. obs: 48286 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 56.99 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.044 / Rrim(I) all: 0.116 / Net I/σ(I): 14.4 / Num. measured all: 338409 / Scaling rejects: 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.78-2.887.20.7040.767197.7
11.13-495.20.0360.999197.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.35 Å48.11 Å
Translation8.35 Å48.11 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: 2.784→48.11 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.09
RfactorNum. reflection% reflection
Rfree0.2594 4560 5.07 %
Rwork0.2028 --
obs0.2057 44958 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.87 Å2 / Biso mean: 64.5029 Å2 / Biso min: 20.33 Å2
Refinement stepCycle: final / Resolution: 2.784→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11190 0 86 52 11328
Biso mean--71.1 48.93 -
Num. residues----1471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711480
X-RAY DIFFRACTIONf_angle_d0.61115551
X-RAY DIFFRACTIONf_chiral_restr0.0471817
X-RAY DIFFRACTIONf_plane_restr0.0032005
X-RAY DIFFRACTIONf_dihedral_angle_d15.3244005
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5962X-RAY DIFFRACTION15.203TORSIONAL
12B5962X-RAY DIFFRACTION15.203TORSIONAL
13C5962X-RAY DIFFRACTION15.203TORSIONAL
14D5962X-RAY DIFFRACTION15.203TORSIONAL
15E5962X-RAY DIFFRACTION15.203TORSIONAL
16F5962X-RAY DIFFRACTION15.203TORSIONAL
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 (%)
2.7837-2.81530.32451290.28612623275291
2.8153-2.84850.3311600.288828372997100
2.8485-2.88320.38421470.271728733020100
2.8832-2.91970.31171750.253228573032100
2.9197-2.95810.31161450.253328232968100
2.9581-2.99860.33121740.263428953069100
2.9986-3.04140.32761360.271128242960100
3.0414-3.08680.34231490.251428973046100
3.0868-3.13510.34111730.259628062979100
3.1351-3.18650.30771530.239828713024100
3.1865-3.24140.3311410.235628452986100
3.2414-3.30030.29181460.222428492995100
3.3003-3.36380.28811390.224828893028100
3.3638-3.43240.34081220.213228542976100
3.4324-3.5070.2991440.219629033047100
3.507-3.58860.291520.217928563008100
3.5886-3.67830.28871430.2128372980100
3.6783-3.77770.30911520.192428603012100
3.7777-3.88880.21221390.189828993038100
3.8888-4.01430.22651850.177628193004100
4.0143-4.15770.22921630.172928493012100
4.1577-4.32410.23561560.174728463002100
4.3241-4.52070.17751510.161928332984100
4.5207-4.75880.23451360.171128582994100
4.7588-5.05670.18751580.162328352993100
5.0567-5.44660.2351550.180228703025100
5.4466-5.99380.24651520.212528573009100
5.9938-6.8590.27081800.215927912971100
6.859-8.63350.22411600.187228563016100
8.6335-48.11750.24521450.19072844298999
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)
13.31991.46432.36713.48011.65152.555-0.3135-0.316-0.17160.10510.3045-0.20390.12580.57020.02170.70350.08640.06980.9820.09530.743254.294941.708520.4574
26.5843-1.17550.45835.94110.72833.5981-0.0238-1.0097-0.44580.71330.0827-0.95360.47311.1764-0.08120.46040.1508-0.03970.80430.06580.433949.488665.72826.6043
36.22633.24340.60966.12860.34056.5973-0.0605-0.27550.1714-0.07280.09690.21250.22250.3147-0.03640.25940.0627-0.00650.42360.1220.3140.403771.615623.8842
40.67660.3011-0.27144.6253-2.98573.4503-0.01540.1328-0.1016-0.3169-0.0661-0.21010.28310.11590.10610.39780.03830.05350.3425-0.04550.327226.229231.813-4.6547
56.74240.7129-0.99595.0913-0.5395.0062-0.06070.0390.43310.1896-0.21320.4811-0.4005-0.41070.29560.42190.04670.05080.2516-0.01120.389519.845231.37483.5113
62.0375-0.28892.23084.66031.89657.9429-0.05030.0524-0.0873-0.05120.03110.02120.23220.18280.00310.23560.02730.03560.31840.06980.335429.247560.9045-3.853
71.1824-1.0954-0.81819.27380.99912.5775-0.1134-0.4170.34360.66860.3555-0.4767-0.07460.0097-0.23860.36050.1037-0.06730.5593-0.05350.400122.2207104.0387-18.7216
82.3551-1.39471.67093.87270.95955.6317-0.16570.15480.1049-0.07460.1014-0.1114-0.17560.15490.06440.2189-0.00280.03050.32070.08130.274818.872377.1143-4.8453
93.10430.5534-1.89554.6935-4.13615.270.12960.00260.51720.1634-0.1957-0.3507-0.2505-0.05750.09570.3596-0.0064-0.01310.3613-0.01670.43237.7815109.123822.9423
100.6324-0.39-0.00846.7207-5.35843.73380.08880.15210.3058-0.5737-0.1772-0.08090.41150.17320.11630.438-0.01920.00310.3913-0.02610.4968.3983102.831416.4211
115.13480.48180.69776.34622.24213.683-0.0934-0.1846-0.0593-0.0334-0.09140.07370.0465-0.15380.1970.2354-0.02060.02120.28120.03240.264517.895881.917828.1701
124.2449-6.09843.52379.9951-4.21042.56030.36670.249-0.2392-0.3576-0.22890.28270.1120.1042-0.08850.35250.00240.05060.43460.02380.471847.2923112.639810.6276
135.7193-3.04020.92446.5746-0.39615.4725-0.0257-1.1318-1.20590.52750.37920.89540.6813-0.467-0.36560.55750.10210.11070.65630.17470.848539.3461113.919117.4152
141.51270.72772.05174.76850.72943.6747-0.14320.1232-0.0067-0.15290.2864-0.3235-0.05640.5007-0.13270.2385-0.06770.05980.42770.00190.332346.437983.487513.4726
152.0803-1.7672-0.34366.0775-1.13613.60240.0820.1068-0.1354-0.5896-0.2485-0.08540.84570.20570.150.63150.01970.08180.35720.06060.330412.70937.717834.5525
16-0.0946-0.72640.09665.2508-2.49371.14860.18660.28840.2995-0.8667-0.511-0.99590.31610.47920.23590.51850.0250.15350.66770.09960.567520.022143.370833.4391
179.09391.71791.25293.9420.41364.1383-0.0684-0.228-0.1735-0.01120.04130.01770.3533-0.17120.03550.3066-0.00220.04840.20290.06310.237512.463464.850523.0067
180.50.5078-0.60255.14571.0711.7013-0.1102-0.3218-0.52390.90240.098-0.460.62910.3539-0.00220.89920.33480.06980.86560.16530.92653.023740.845626.2045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 96 through 177 )E96 - 177
2X-RAY DIFFRACTION2chain 'E' and (resid 178 through 225 )E178 - 225
3X-RAY DIFFRACTION3chain 'E' and (resid 226 through 259 )E226 - 259
4X-RAY DIFFRACTION4chain 'F' and (resid 2 through 114 )F2 - 114
5X-RAY DIFFRACTION5chain 'F' and (resid 115 through 177 )F115 - 177
6X-RAY DIFFRACTION6chain 'F' and (resid 178 through 260 )F178 - 260
7X-RAY DIFFRACTION7chain 'A' and (resid 2 through 177 )A2 - 177
8X-RAY DIFFRACTION8chain 'A' and (resid 178 through 259 )A178 - 259
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 114 )B2 - 114
10X-RAY DIFFRACTION10chain 'B' and (resid 115 through 189 )B115 - 189
11X-RAY DIFFRACTION11chain 'B' and (resid 190 through 259 )B190 - 259
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 115 )C2 - 115
13X-RAY DIFFRACTION13chain 'C' and (resid 116 through 177 )C116 - 177
14X-RAY DIFFRACTION14chain 'C' and (resid 178 through 259 )C178 - 259
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 115 )D2 - 115
16X-RAY DIFFRACTION16chain 'D' and (resid 116 through 189 )D116 - 189
17X-RAY DIFFRACTION17chain 'D' and (resid 190 through 259 )D190 - 259
18X-RAY DIFFRACTION18chain 'E' and (resid 2 through 95 )E2 - 95

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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