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- PDB-3fpg: Crystal Structure of E81Q mutant of MtNAS -

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Basic information

Entry
Database: PDB / ID: 3fpg
TitleCrystal Structure of E81Q mutant of MtNAS
ComponentsPutative uncharacterized protein
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE / thermonicotianamine / nicotianamine
Function / homology
Function and homology information


nicotianamine synthase activity / nicotianamine biosynthetic process / identical protein binding
Similarity search - Function
Nicotianamine synthase protein / Nicotianamine synthase (NAS)-like family profile. / Nicotianamine synthase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Methyltransferase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsDreyfus, C. / Pignol, D. / Arnoux, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystallographic snapshots of iterative substrate translocations during nicotianamine synthesis in Archaea
Authors: Dreyfus, C. / Lemaire, D. / Mari, S. / Pignol, D. / Arnoux, P.
History
DepositionJan 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0624
Polymers67,6992
Non-polymers3622
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-10 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.696, 67.498, 147.652
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein / MtNAS


Mass: 33849.734 Da / Num. of mol.: 2 / Mutation: E81Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: MTH675 / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O26771
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 3350, 200mM NaK Tartrate, 100mM BisTrisPropane, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9685 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9685 Å / Relative weight: 1
ReflectionResolution: 2→67.574 Å / Num. all: 43159 / Num. obs: 36210 / % possible obs: 83.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 4.574
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.114.90.5541.32666154480.55487
2.11-2.2450.3841.92525550680.38485.7
2.24-2.3950.2592.72367847260.25985.1
2.39-2.5850.1953.62213344100.19584.6
2.58-2.835.10.1464.72026440000.14683.7
2.83-3.1650.1125.71820236060.11283.1
3.16-3.6550.096.81595931760.0982.7
3.65-4.474.90.0837.31317726780.08381.5
4.47-6.324.80.0777.8961620190.07779.4
6.32-67.575.20.0629.4557010790.06273.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FPE

3fpe


Resolution: 2→32.39 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.265 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1850 5.1 %RANDOM
Rwork0.193 ---
obs0.196 36177 82.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.11 Å2 / Biso mean: 22.948 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2→32.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 20 537 4779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224326
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.9745851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5285526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38323.039204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09815760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3211540
X-RAY DIFFRACTIONr_chiral_restr0.1290.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023250
X-RAY DIFFRACTIONr_nbd_refined0.2590.22225
X-RAY DIFFRACTIONr_nbtor_refined0.3210.23025
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.2385
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.6610.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3220.231
X-RAY DIFFRACTIONr_mcbond_it1.3241.52686
X-RAY DIFFRACTIONr_mcangle_it1.89924252
X-RAY DIFFRACTIONr_scbond_it3.57831827
X-RAY DIFFRACTIONr_scangle_it5.044.51599
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 145 -
Rwork0.216 2603 -
all-2748 -
obs--86.06 %

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