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- PDB-8cp3: Apo-LarE in complex with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 8cp3
TitleApo-LarE in complex with AMP-PNP
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 / homology
Function and homology information


sulfurtransferase activity / 4 iron, 4 sulfur cluster binding / nucleotide binding / metal ion 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / BETA-MERCAPTOETHANOL / NAD/GMP synthase domain-containing protein
Similarity search - Component
Biological speciesMethanococcus maripaludis S2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsZecchin, P. / Pecqueur, L. / 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
DepositionMar 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.journal_volume / _citation.year ..._citation.journal_volume / _citation.year / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_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: NAD_synthase domain-containing protein
B: NAD_synthase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,16113
Polymers62,3242
Non-polymers1,83711
Water54030
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-104 kcal/mol
Surface area25120 Å2
Unit cell
Length a, b, c (Å)144.810, 144.810, 193.640
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21A-411-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 84 or (resid 85...
d_2ens_1(chain "B" and (resid 3 through 92 or (resid 93...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ILEILETHRTHRAA3 - 8814 - 99
d_12ASPASPCYSCYSAA91 - 174102 - 185
d_13ILEILESERSERAA184 - 185195 - 196
d_14GLUGLULEULEUAA187 - 209198 - 220
d_15VALVALARGARGAA211 - 212222 - 223
d_16LEULEUPHEPHEAA214 - 257225 - 268
d_17BMEBMEBMEBMEAD302
d_21ILEILECYSCYSBB3 - 17414 - 185
d_22ILEILEPHEPHEBB184 - 248195 - 259
d_23VALVALPHEPHEBB251 - 257262 - 268
d_24BMEBMEBMEBMEBI303

NCS oper: (Code: givenMatrix: (-0.963380899049, 0.129855079579, 0.23459518677), (0.137722651569, -0.511048168958, 0.848446957829), (0.230064587872, 0.849686664196, 0.474450058588)Vector: -136. ...NCS oper: (Code: given
Matrix: (-0.963380899049, 0.129855079579, 0.23459518677), (0.137722651569, -0.511048168958, 0.848446957829), (0.230064587872, 0.849686664196, 0.474450058588)
Vector: -136.798395369, 15.4642855794, 18.9497295511)

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis S2 (archaea) / Gene: MMP1239 / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6LXV7

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Non-polymers , 5 types, 41 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M Ammonium Sulfate, 2 % PEG 400, 0.1 M Hepes pH 7.5, 5 mM AMP-PNP.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2021 / Details: U20
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.35→48.18 Å / Num. obs: 32562 / % possible obs: 99.7 % / Redundancy: 20.7 % / Biso Wilson estimate: 79.3 Å2 / CC1/2: 1 / Rrim(I) all: 0.067 / Net I/σ(I): 25.46
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
6.99-48.1898.39132510.028199.5
4.97-6.9969.25227610.0431100
4.06-4.9769.29288210.0441100
3.52-4.0645.7333970.9990.0681100
3.15-3.5225.0838420.9980.1271100
2.88-3.1511.4742170.9910.2841100
2.67-2.885.4245970.9620.5891100
2.49-2.672.3248980.8211.2241100
2.35-2.490.9551280.5012.432198.5

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Processing

Software
NameVersionClassification
MxCuBEMars, 2021data collection
XDSMars, 2021data reduction
XDSMars, 2021data scaling
MOLREPMars, 2021phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→45.16 Å / SU ML: 0.3742 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9863
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2503 1627 5 %
Rwork0.2317 30897 -
obs0.2327 32524 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.15 Å2
Refinement stepCycle: LAST / Resolution: 2.35→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 106 30 3852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00843878
X-RAY DIFFRACTIONf_angle_d1.09495248
X-RAY DIFFRACTIONf_chiral_restr0.0599621
X-RAY DIFFRACTIONf_plane_restr0.0075649
X-RAY DIFFRACTIONf_dihedral_angle_d14.96041397
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 6.68974795405 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.420.38011290.31312441X-RAY DIFFRACTION95.97
2.42-2.50.30331350.29822557X-RAY DIFFRACTION100
2.5-2.590.35051350.35732562X-RAY DIFFRACTION99.96
2.59-2.690.33941340.30512551X-RAY DIFFRACTION100
2.69-2.810.32731360.25212573X-RAY DIFFRACTION100
2.81-2.960.28431350.24472566X-RAY DIFFRACTION100
2.96-3.150.28881350.26822571X-RAY DIFFRACTION100
3.15-3.390.31360.2532582X-RAY DIFFRACTION100
3.39-3.730.26171350.21632574X-RAY DIFFRACTION100
3.73-4.270.21011380.20722608X-RAY DIFFRACTION100
4.27-5.380.21331370.20382605X-RAY DIFFRACTION100
5.38-45.160.24561420.23782707X-RAY DIFFRACTION99.82
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)
13.27606992285-0.216925928255-0.8775326259753.240253390521.24777561113.256323090720.020744737947-0.1117705999990.1765955334210.1320947638270.0782700514475-0.203502510925-0.195566665390.3977167698210.0002787557833940.6772023250150.002095965643830.002532195950010.698517653310.04549159358130.630870465822-85.40310.00312.524
20.4422346591620.31718928113-0.3675389119640.37656546467-0.121621653370.4038500390880.522826996797-0.413491531691.177362417940.06891571786360.521982801734-0.667120820155-0.178668294671-0.3332475583759.54301801912E-51.351146553820.0651835435115-0.08907868474611.73665211492-0.186583303271.42952222701-56.60926.32232.008
32.517326163720.8610103610780.3499414981463.414807231990.9802677167282.640119851650.0785397845475-0.284672102567-0.1929716187310.327511239336-0.0899123845479-0.1459037487950.128571539117-0.25641760237-7.98271387338E-60.701312240501-0.0231003128696-0.06281248770330.7469773671390.04947602331010.773204670239-49.2229.67713.116
40.308297182737-0.3472429438430.05114973850470.395148409311-0.09365830673960.07123876246960.0986954354211-0.736508333318-0.2647601010611.900639624120.2953982083560.255094965060.5639605471910.2573973024494.46186484366E-51.74874984523-0.141521576570.1373751403551.9956040829-0.00937646211941.3016136008-70.34221.144.512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:175 )A3 - 175
2X-RAY DIFFRACTION2( CHAIN A AND RESID 184:257 )A184 - 257
3X-RAY DIFFRACTION3( CHAIN B AND RESID 0:174 )B0 - 174
4X-RAY DIFFRACTION4( CHAIN B AND RESID 183:259 )B183 - 259

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