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- PDB-8cnz: mmLarE-[4Fe-4S] phased by Fe-SAD -

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Basic information

Entry
Database: PDB / ID: 8cnz
TitlemmLarE-[4Fe-4S] phased by Fe-SAD
ComponentsNAD_synthase domain-containing protein
KeywordsTRANSFERASE / LAR / SULFUR TRANSFERASE / LARE / AMP / 4FE-4S / THIOLATION / [FE-S] CLUSTER / IRON-SULFUR CLUSTER / PP-LOOP / ATP PYROPHOSPHATASE / LACTATE / LACTATE RACEMIZATION
Function / homologyPyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase LarE / sulfurtransferase activity / NAD/GMP synthase / NAD synthase / Rossmann-like alpha/beta/alpha sandwich fold / IODIDE ION / IRON/SULFUR CLUSTER / NAD/GMP synthase domain-containing protein
Function and homology information
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.6 Å
AuthorsPecqueur, L. / Zecchin, P. / Golinelli-Pimpaneau, B.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LABX-0011 France
CitationJournal: Protein Sci. / Year: 2024
Title: Structure-based insights into the mechanism of [4Fe-4S]-dependent sulfur insertase LarE.
Authors: Zecchin, P. / Pecqueur, L. / Oltmanns, J. / Velours, C. / Schunemann, V. / Fontecave, M. / Golinelli-Pimpaneau, B.
History
DepositionFeb 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD_synthase domain-containing protein
B: NAD_synthase domain-containing protein
C: NAD_synthase domain-containing protein
D: NAD_synthase domain-containing protein
E: NAD_synthase domain-containing protein
F: NAD_synthase domain-containing protein
G: NAD_synthase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,28023
Polymers218,1337
Non-polymers3,14616
Water0
1
A: NAD_synthase domain-containing protein
hetero molecules

A: NAD_synthase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3528
Polymers62,3242
Non-polymers1,0286
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3240 Å2
ΔGint-75 kcal/mol
Surface area25120 Å2
MethodPISA
2
B: NAD_synthase domain-containing protein
D: NAD_synthase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3528
Polymers62,3242
Non-polymers1,0286
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-71 kcal/mol
Surface area25720 Å2
MethodPISA
3
C: NAD_synthase domain-containing protein
E: NAD_synthase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0986
Polymers62,3242
Non-polymers7744
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-73 kcal/mol
Surface area25340 Å2
MethodPISA
4
F: NAD_synthase domain-containing protein
G: NAD_synthase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1545
Polymers62,3242
Non-polymers8303
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-48 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.516, 209.215, 195.799
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
NAD_synthase domain-containing protein / LarE / ATP-dependent sacrificial sulfur transferase LarE / NAD_synthase domain-containing protein


Mass: 31161.916 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Gene: MMP1239,larE / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6LXV7
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestN

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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: 4.42 Å3/Da / Density % sol: 72.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 4.1 M NaCl, 0.1 M Hepes pH 7.5, 0.1M NaI.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857, 1.74013
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978571
21.740131
ReflectionResolution: 3.145→113.688 Å / Num. obs: 44021 / % possible obs: 93.7 % / Redundancy: 5.98 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways through the data processing procedure (rejection of overloaded or too partial reflections, outlier/misfit rejection during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.996 / Rmerge(I) obs: 0.1695 / Rpim(I) all: 0.0755 / Rrim(I) all: 0.186 / Net I/σ(I): 7 / Num. measured all: 263306
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
9.99-113.6885.310.060422.791168011680220022000.9960.02810.066998.3
7.904-9.995.50.071819.541209412094220022000.9950.0330.079399.5
6.885-7.9045.850.105613.861288912889220222020.9920.04670.115899.8
6.243-6.8856.030.16069.51327213272220122010.9850.07030.175699.8
5.785-6.2435.680.19137.881251812518220222020.9770.08650.210699.9
5.439-5.7855.740.1967.711262012620220022000.9780.08880.215899.9
5.161-5.4395.440.21057.011197011970220122010.9720.09730.232598.9
4.932-5.1615.70.23796.371254012540220122010.9740.10750.2618100
4.741-4.9325.80.23656.511276812768220222020.9760.10620.259999.9
4.574-4.7415.90.26376.021298212982220122010.9690.1180.289699.8
4.428-4.57460.30665.351320413204220022000.9620.13560.335998.6
4.294-4.4286.150.36544.731354713547220122010.9570.16040.399795.3
4.171-4.2946.250.40924.351377213772220222020.9350.17840.447292.8
4.058-4.1716.410.50083.741409614096220022000.920.21530.545892.1
3.95-4.0586.360.54723.41401414014220422040.8950.23610.596894.8
3.848-3.956.10.68212.751341713417220022000.8090.30140.746997.6
3.748-3.8486.420.76912.481412614126220022000.8250.32920.837697.2
3.635-3.7486.230.80252.331371213712220122010.8010.34960.876589.5
3.482-3.6356.360.91142.111400214002220222020.7250.39160.993573.3
3.145-3.4826.41.16691.661408314083220122010.6140.49931.271365.8

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Processing

Software
NameVersionClassification
autoPROC1.0.5 20200918data processing
XDSJan 31, 2020data reduction
Aimless0.7.4data scaling
STARANISO2.3.46data scaling
SHELXCD2013/2phasing
PHASER2.8.3phasing
PARROT1.0.4phasing
BUSTER2.10.4refinement
RefinementMethod to determine structure: SAD / Resolution: 3.6→55.37 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.604
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 2006 -RANDOM
Rwork0.2527 ---
obs0.2541 40205 89.7 %-
Displacement parametersBiso mean: 118.23 Å2
Baniso -1Baniso -2Baniso -3
1-5.0857 Å20 Å20 Å2
2---7.5766 Å20 Å2
3---2.4909 Å2
Refine analyzeLuzzati coordinate error obs: 0.58 Å
Refinement stepCycle: LAST / Resolution: 3.6→55.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14378 0 65 0 14443
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00714657HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9219750HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5451SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2465HARMONIC5
X-RAY DIFFRACTIONt_it14657HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2013SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance21HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact10955SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion19.36
LS refinement shellResolution: 3.6→3.65 Å
RfactorNum. reflection% reflection
Rfree0.3617 32 -
Rwork0.3166 --
obs0.3183 805 49.35 %
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)
110.9172-1.1526-1.42426.35741.88146.94590.4210.04450.10120.0445-0.03380.29230.10120.2923-0.3872-0.27970.2526-0.2051-0.1684-0.2231-0.123235.058528.5812-47.2613
212.08390.30333.49215.06260.04686.11540.45660.0291.08850.0290.15390.35971.08850.3597-0.61050.10910.0099-0.304-0.52660.072-0.09566.780416.1342-42.3959
311.1582-2.61772.021510.09380.30456.05450.10030.20180.08640.20180.2360.45780.08640.4578-0.3363-0.372-0.02550.0309-0.2458-0.0857-0.204241.652950.767-23.1962
47.45613.32982.61927.35710.13099.51190.31090.98660.70090.98660.23060.1880.70090.188-0.5416-0.0504-0.2231-0.1106-0.18260.1237-0.483716.607540.3306-8.6593
511.60371.20692.31916.7501-0.31317.4575-0.5738-0.1522-0.3146-0.15220.20750.4797-0.31460.47970.3663-0.2915-0.0996-0.2939-0.37620.2198-0.179740.689484.1103-24.3102
65.16943.5792-1.84319.78520.32135.9541-0.22171.0877-0.70291.0877-0.20470.0647-0.70290.06470.42640.0150.0825-0.304-0.2331-0.3040.102816.32283.1729-6.0169
77.27351.2547-3.13294.7209-1.52929.9870.11250.18250.16310.18250.1878-0.20040.1631-0.2004-0.3003-0.3484-0.26350.04650.14430.304-0.135-25.160731.6283-18.3242
88.85591.02544.77087.62660.11249.15510.29221.01891.08851.0189-0.0069-1.08851.0885-1.0885-0.28530.0486-0.2914-0.1463-0.36440.1976-0.2215.10827.5584-16.3627
910.59720.07510.57078.38670.302910.5046-0.41940.9821-0.39580.98210.342-1.0885-0.3958-1.08850.0774-0.14640.18330.11320.6079-0.0657-0.2392-21.222960.5658-2.6938
108.03753.61531.74287.7821-0.776710.6213-0.4781.0651-0.21081.0651-0.1325-0.4215-0.2108-0.42150.6105-0.12450.0774-0.1186-0.0191-0.1976-0.34648.803767.00360.0869
117.38143.38473.50558.9797-0.97986.5456-0.2851-0.4189-0.1653-0.4189-0.22010.203-0.16530.2030.5052-0.1091-0.2076-0.304-0.17650.3040.238733.5605101.304-52.1371
126.8984-3.08925.820815.3230.58511.6803-0.05170.6421-1.08850.64210.45070.4337-1.08850.4337-0.3990.085-0.1412-0.304-0.4264-0.07620.60797.8654111.093-37.1591
139.1251-4.2936-0.05589.26312.47068.0863-0.55140.8251-0.78260.82510.3902-0.8618-0.7826-0.86180.16120.19380.304-0.3040.1643-0.3040.3232-25.554390.9744-15.1799
146.55961.92615.82083.40482.47598.32470.01070.8457-1.08850.8457-0.2602-0.0007-1.0885-0.00070.24950.2930.0713-0.304-0.2924-0.3040.53562.6161104.026-20.3257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|6 - A|164 }A6 - 164
2X-RAY DIFFRACTION2{ A|186 - A|259 }A186 - 259
3X-RAY DIFFRACTION3{ B|6 - B|164 }B6 - 164
4X-RAY DIFFRACTION4{ B|186 - B|259 }B186 - 259
5X-RAY DIFFRACTION5{ C|4 - C|164 }C4 - 164
6X-RAY DIFFRACTION6{ C|186 - C|259 }C186 - 259
7X-RAY DIFFRACTION7{ D|4 - D|164 }D4 - 164
8X-RAY DIFFRACTION8{ D|186 - D|259 }D186 - 259
9X-RAY DIFFRACTION9{ E|5 - E|164 }E5 - 164
10X-RAY DIFFRACTION10{ E|186 - E|259 }E186 - 259
11X-RAY DIFFRACTION11{ F|7 - F|164 }F7 - 164
12X-RAY DIFFRACTION12{ F|186 - F|259 }F186 - 259
13X-RAY DIFFRACTION13{ G|7 - G|164 }G7 - 164
14X-RAY DIFFRACTION14{ G|186 - G|259 }G186 - 259

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