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- PDB-6c1w: A tethered niacin-derived pincer complex with a nickel-carbon or ... -

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Basic information

Entry
Database: PDB / ID: 6c1w
TitleA tethered niacin-derived pincer complex with a nickel-carbon or sulfite-carbon bond in lactate racemase
ComponentsLactate racemase
KeywordsISOMERASE / Lar / nickel transferase / LarA / nickel / lactate / lactate racemization / lactate racemase / sulfite / sulfite-bond / pincer / cofactor
Function / homology
Function and homology information


lactate racemase / lactate racemase activity / metal ion binding
Similarity search - Function
LarA, C-terminal domain / LarA, N-terminal domain / : / : / : / Lactate racemase C-terminal domain / LarA-like, N-terminal / LarA-like, C-terminal domain / Lactate racemase N-terminal domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 ...LarA, C-terminal domain / LarA, N-terminal domain / : / : / : / Lactate racemase C-terminal domain / LarA-like, N-terminal / LarA-like, C-terminal domain / Lactate racemase N-terminal domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4EY / Chem-ENJ / NICKEL (II) ION / SULFITE ION / Lactate racemase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.398 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: Biochemistry / Year: 2018
Title: Lactate Racemase Nickel-Pincer Cofactor Operates by a Proton-Coupled Hydride Transfer Mechanism.
Authors: Rankin, J.A. / Mauban, R.C. / Fellner, M. / Desguin, B. / McCracken, J. / Hu, J. / Varganov, S.A. / Hausinger, R.P.
History
DepositionJan 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 1.5Oct 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 2.0May 1, 2024Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactate racemase
B: Lactate racemase
C: Lactate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,17226
Polymers142,1093
Non-polymers3,06323
Water1,964109
1
A: Lactate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2907
Polymers47,3701
Non-polymers9206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lactate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,59311
Polymers47,3701
Non-polymers1,22410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lactate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2898
Polymers47,3701
Non-polymers9197
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.365, 157.897, 158.988
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Lactate racemase / / Lar / Lactate racemization operon protein LarA


Mass: 47369.633 Da / Num. of mol.: 3 / Mutation: C-terminal fusion to ASWSHPQFEK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: larA, lp_0104 / Plasmid: pGIR112 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ3900 / References: UniProt: F9USS9, lactate racemase

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Non-polymers , 6 types, 132 molecules

#2: Chemical ChemComp-ENJ / (4S)-5-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-4-sulfo-1,4-dihydropyridine-3-carbothioic S-acid


Mass: 477.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16NO11PS3
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-4EY / 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium / Dithiodinicotinic acid mononucleotide


Mass: 396.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO8PS2
#6: Chemical ChemComp-SO3 / SULFITE ION / Sulfite


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.07 Å3/Da / Density % sol: 59.89 % / Mosaicity: 0.407 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M bis-Tris buffer, pH 6.5, with 2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 68698 / % possible obs: 99.2 % / Redundancy: 13.2 % / Biso Wilson estimate: 44.96 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.043 / Rrim(I) all: 0.138 / Χ2: 0.949 / Net I/σ(I): 6 / Num. measured all: 907118
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.4-2.4911.366690.7970.4840.67797.7
2.49-2.5912.267070.8560.3730.71398.5
2.59-2.712.767630.9210.2530.76698.80.8850.922
2.7-2.8513.167750.9630.1720.82799.10.6090.634
2.85-3.0213.468390.9810.1090.96299.20.390.406
3.02-3.2613.768530.990.0691.09499.60.2460.256
3.26-3.5814.168610.9940.0461.00499.50.1640.17
3.58-4.113.369410.9950.0361.04899.70.1260.131
4.1-5.1714.569990.9970.0241.0799.90.0870.09
5.17-4013.672910.9980.021.19399.70.070.073

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HUQ
Resolution: 2.398→38.545 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 33.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2627 6283 4.8 %
Rwork0.2063 124598 -
obs0.2091 130881 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.24 Å2 / Biso mean: 53.8249 Å2 / Biso min: 27.44 Å2
Refinement stepCycle: final / Resolution: 2.398→38.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9880 0 163 109 10152
Biso mean--55.66 48.31 -
Num. residues----1296
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 (%)
2.3984-2.42560.40532170.3374057427498
2.4256-2.45420.38992150.32444052426798
2.4542-2.48410.32971930.31594119431296
2.4841-2.51550.39861760.3164136431299
2.5155-2.54860.42081840.31254235441999
2.5486-2.58350.35721850.2874058424397
2.5835-2.62040.36231900.27344147433799
2.6204-2.65950.38091990.27254198439798
2.6595-2.70110.3251720.25754143431599
2.7011-2.74540.29341970.25274185438299
2.7454-2.79270.33551780.25884145432398
2.7927-2.84350.31222390.266341334372100
2.8435-2.89810.31622330.26634147438099
2.8981-2.95730.34271840.260841654349100
2.9573-3.02150.37842250.26164203442899
3.0215-3.09180.34011780.275741804358100
3.0918-3.16910.37072240.25384163438799
3.1691-3.25470.34772370.242941604397100
3.2547-3.35040.32562140.23074135434999
3.3504-3.45850.2682340.22541954429100
3.4585-3.5820.26632030.21744149435299
3.582-3.72540.28482280.21064158438699
3.7254-3.89480.23482030.186641824385100
3.8948-4.09990.21832420.168941754417100
4.0999-4.35640.21242290.154441674396100
4.3564-4.69220.19142030.142142094412100
4.6922-5.16340.18662190.144841694388100
5.1634-5.90830.21162300.173141734403100
5.9083-7.43510.24542620.171941424404100
7.4351-38.54950.17451900.15054118430898

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