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- PDB-3fph: Crystal Structure of E81Q mutant of MtNAS in complex with L-Glutamate -

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Basic information

Entry
Database: PDB / ID: 3fph
TitleCrystal Structure of E81Q mutant of MtNAS in complex with L-Glutamate
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
GLUTAMIC ACID / Methyltransferase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)68,0406
Polymers67,6992
Non-polymers3404
Water12,845713
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-33 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.198, 69.785, 146.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 22% PEG 3350, 400mM NaBr, pH 8, 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: Jun 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9685 Å / Relative weight: 1
ReflectionResolution: 1.8→66.227 Å / Num. all: 63178 / Num. obs: 61535 / % possible obs: 97.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 5.415
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.94.40.4681.64025691610.46899.9
1.9-2.014.40.2562.93818186670.25699.7
2.01-2.154.40.1425.33579280940.14299.4
2.15-2.324.50.0997.23339174820.09998.6
2.32-2.554.50.0788.53081469130.07898.4
2.55-2.854.50.05311.92757361690.05397.4
2.85-3.294.50.04711.92420354250.04796.3
3.29-4.024.40.0678.11984145150.06794.8
4.02-5.694.20.06191449434130.06191.6
5.69-69.844.50.03319.2756516960.03379.4

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Processing

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

3fpe


Resolution: 1.8→60.3 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.733 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3067 5 %RANDOM
Rwork0.191 ---
obs0.193 61496 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.65 Å2 / Biso mean: 28.107 Å2 / Biso min: 12.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.8→60.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 22 713 4957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224344
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9735872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4795526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99823.173208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16215768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8431540
X-RAY DIFFRACTIONr_chiral_restr0.1330.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023282
X-RAY DIFFRACTIONr_nbd_refined0.2510.22272
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2564
X-RAY DIFFRACTIONr_metal_ion_refined0.0330.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3990.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3340.245
X-RAY DIFFRACTIONr_mcbond_it1.0081.52640
X-RAY DIFFRACTIONr_mcangle_it1.8524272
X-RAY DIFFRACTIONr_scbond_it3.27331748
X-RAY DIFFRACTIONr_scangle_it5.2674.51600
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 218 -
Rwork0.258 4454 -
all-4672 -
obs--99.87 %

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