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- PDB-6bwo: LarC2, the C-terminal domain of a cyclometallase involved in the ... -

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Basic information

Entry
Database: PDB / ID: 6bwo
TitleLarC2, the C-terminal domain of a cyclometallase involved in the synthesis of the NPN cofactor of lactate racemase, apo form
ComponentsPyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
KeywordsMETAL BINDING PROTEIN / Lar / nickel transferase / LarC / hexamer / trimer / CTP / nickel / lactate / lactate racemization / lactate racemase
Function / homologypyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel chelatase / Nickel insertion protein / Nickel insertion protein / nickel cation binding / protein maturation / lyase activity / Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
Function and homology information
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 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: J. Biol. Chem. / Year: 2018
Title: Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase.
Authors: Desguin, B. / Fellner, M. / Riant, O. / Hu, J. / Hausinger, R.P. / Hols, P. / Soumillion, P.
History
DepositionDec 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
B: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein


Theoretical massNumber of molelcules
Total (without water)33,6382
Polymers33,6382
Non-polymers00
Water1,76598
1
A: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
B: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

A: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
B: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

A: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
B: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein


Theoretical massNumber of molelcules
Total (without water)100,9156
Polymers100,9156
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area24400 Å2
ΔGint-130 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.900, 96.900, 96.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-538-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and ((resid 272 through 273 and (name N...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNchain AAA272 - 4151 - 144
21ALAALA(chain B and ((resid 272 through 273 and (name N...BB272 - 2731 - 2
22GLNGLN(chain B and ((resid 272 through 273 and (name N...BB272 - 4151 - 144
23GLNGLN(chain B and ((resid 272 through 273 and (name N...BB272 - 4151 - 144
24GLNGLN(chain B and ((resid 272 through 273 and (name N...BB272 - 4151 - 144
25GLNGLN(chain B and ((resid 272 through 273 and (name N...BB272 - 4151 - 144

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Components

#1: Protein Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein / P2TMN nickel insertion protein / Lactate racemase accessory protein LarC / Lactate racemase ...P2TMN nickel insertion protein / Lactate racemase accessory protein LarC / Lactate racemase activation protein LarC / Lactate racemase maturation protein LarC / Lactate racemization operon protein LarC / Nickel-pincer cofactor biosynthesis protein LarC


Mass: 16819.143 Da / Num. of mol.: 2 / Fragment: LarC2 domain of LarC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Plasmid: pET-22b_pGIR051 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: F9UST1
#2: 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: 2.25 Å3/Da / Density % sol: 45.43 % / Mosaicity: 0.14 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.13 ul ~13 mg/ml LarC (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 0.13 ul of reservoir solution. Sitting drop reservoir contained 100 ul of 0.15 M DL-Malic acid, 20% w/v Polyethylene ...Details: 0.13 ul ~13 mg/ml LarC (100 mM Tris-HCl pH 7.5, 300 mM NaCl) mixed with 0.13 ul of reservoir solution. Sitting drop reservoir contained 100 ul of 0.15 M DL-Malic acid, 20% w/v Polyethylene glycol 3,350. Crystal grew within a week. The crystal was soaked for 1 minute in 25% Polyethylene glycol 400, 75% reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.49
ReflectionResolution: 2.03→43.33 Å / Num. obs: 19861 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.044 / Rrim(I) all: 0.112 / Net I/σ(I): 12 / Num. measured all: 124437
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.03-2.086.20.90814400.5530.3950.99297.8
9.07-43.335.80.0392490.9980.0170.04397

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.79 Å39.56 Å
Translation4.79 Å39.56 Å

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Processing

Software
NameVersionClassification
XDS2.99data reduction
Aimless0.5.32data scaling
PHASER2.8.0phasing
PHENIX1.12-2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house SAD model

Resolution: 2.03→39.559 Å / Cross valid method: THROUGHOUT / σ(F): 2.37 / Phase error: 19.92
RfactorNum. reflection% reflection
Rfree0.1935 3823 10.12 %
Rwork0.1395 --
obs0.1519 18884 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.91 Å2 / Biso mean: 34.9423 Å2 / Biso min: 15.44 Å2
Refinement stepCycle: final / Resolution: 2.03→39.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 0 98 2378
Biso mean---38.41 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092320
X-RAY DIFFRACTIONf_angle_d0.9113155
X-RAY DIFFRACTIONf_chiral_restr0.054373
X-RAY DIFFRACTIONf_plane_restr0.006404
X-RAY DIFFRACTIONf_dihedral_angle_d2.7081399
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1350X-RAY DIFFRACTION6.711TORSIONAL
12B1350X-RAY DIFFRACTION6.711TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0302-2.06520.26781820.2521714189690
2.0652-2.10280.27911930.23711735192889
2.1028-2.14320.29531780.23381690186890
2.1432-2.1870.27671890.22121677186689
2.187-2.23450.26491820.21931703188589
2.2345-2.28650.24821860.21151663184989
2.2865-2.34360.23111850.19311689187490
2.3436-2.4070.26441970.19721740193790
2.407-2.47780.2521890.19121685187490
2.4778-2.55780.21621840.18181712189690
2.5578-2.64910.21062000.17791715191590
2.6491-2.75520.23711960.17031716191290
2.7552-2.88050.17931880.14791686187490
2.8805-3.03230.19411950.14541719191490
3.0323-3.22210.21591920.13741715190790
3.2221-3.47070.18271900.12131687187790
3.4707-3.81960.17971970.11251696189388
3.8196-4.37130.17991770.10531612178986
4.3713-5.50370.14981920.0941717190990
5.5037-34.26420.19132010.13971694189589
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)
11.4021-1.0340.39740.8703-1.0795.8345-0.0955-0.0357-0.07830.12430.08830.1181-0.0666-0.16230.01320.1658-0.03240.02830.1190.0080.212934.30730.3441-0.3949
21.28640.27960.48140.56-0.69532.94890.0378-0.2086-0.07490.09120.02660.09780.0867-0.1261-0.08780.1730.01510.05140.1720.01250.197338.2255-3.67684.1217
36.4493-2.7002-0.21413.80611.20292.75220.133-0.229-0.01620.48440.00250.13610.1061-0.2611-0.13430.3687-0.04030.03010.35660.01430.223539.010522.49718.6695
48.75712.81761.11089.38540.17845.7525-0.00440.1920.48840.07760.18720.3353-0.01620.2933-0.20290.23260.03630.03670.35730.01590.235228.839828.540511.9834
53.6009-1.707-0.2252.8957-1.05363.3741-0.12850.2378-0.0801-0.02450.09360.0524-0.2354-0.17520.02290.22240.00750.04190.1906-0.01420.189725.53323.0972-11.8826
66.5207-0.74730.48920.6886-0.2020.9941-0.0755-0.1355-0.02970.050.0780.1438-0.0385-0.06810.00820.223-0.0056-0.00380.1562-0.00890.171828.643320.5614-6.2518
72.14512.10240.91572.51371.33181.91930.04140.00230.22720.04370.00450.3336-0.2081-0.087-0.03660.20780.03080.02950.18450.01940.253420.842826.3517-11.8579
82.65620.9181.45474.3645-3.73177.0902-0.2833-0.0122-0.09870.22190.10890.2393-0.17-0.35330.12980.20880.05010.04620.2755-0.03080.26728.235-0.674-11.7402
96.64260.18321.12189.03311.24224.7706-0.01780.22130.03470.15760.0588-0.43970.36650.1462-0.00370.18170.010.0340.28170.03750.198814.3298-6.5889-0.9519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 272 through 316 )A272 - 316
2X-RAY DIFFRACTION2chain 'A' and (resid 317 through 357 )A317 - 357
3X-RAY DIFFRACTION3chain 'A' and (resid 358 through 387 )A358 - 387
4X-RAY DIFFRACTION4chain 'A' and (resid 388 through 415 )A388 - 415
5X-RAY DIFFRACTION5chain 'B' and (resid 272 through 287 )B272 - 287
6X-RAY DIFFRACTION6chain 'B' and (resid 288 through 327 )B288 - 327
7X-RAY DIFFRACTION7chain 'B' and (resid 328 through 357 )B328 - 357
8X-RAY DIFFRACTION8chain 'B' and (resid 358 through 387 )B358 - 387
9X-RAY DIFFRACTION9chain 'B' and (resid 388 through 415 )B388 - 415

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