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- PDB-3fpf: Crystal Structure of MtNAS in complex with MTA and tNA -

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Basic information

Entry
Database: PDB / ID: 3fpf
TitleCrystal Structure of MtNAS in complex with MTA and tNA
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 / 5'-DEOXY-5'-METHYLTHIOADENOSINE / Chem-TNA / Methyltransferase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 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 1, 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_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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,1558
Polymers67,7012
Non-polymers1,4536
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-10 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.410, 68.740, 146.300
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: 33850.719 Da / Num. of mol.: 2
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-TNA / N-[(3S)-3-{[(3S)-3-amino-3-carboxypropyl]amino}-3-carboxypropyl]-L-glutamic acid / thermonicotianamine


Mass: 349.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H23N3O8
#3: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3S
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 3350, 400mM NaBr, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.66→44.766 Å / Num. all: 77390 / Num. obs: 76848 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 7.034
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.66-1.753.70.2822.641475111600.28299.8
1.75-1.863.90.2013.741462106120.201100
1.86-1.983.90.1624.43895299240.16299.9
1.98-2.143.90.1066.73667693420.10699.9
2.14-2.353.90.09573319785480.09599.8
2.35-2.623.90.0669.93024677730.06699.7
2.62-3.033.90.05910.32644868490.05999.3
3.03-3.713.80.0619.72184557650.06198.6
3.71-5.253.60.04114.71599944700.04197.3
5.25-44.773.70.03212.7884924050.03292.1

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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
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FPE

3fpe


Resolution: 1.66→44.75 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.807 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3844 5 %RANDOM
Rwork0.199 ---
obs0.2 76848 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61 Å2 / Biso mean: 18.002 Å2 / Biso min: 6.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.66→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 90 550 4862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224398
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9925950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4165526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78723.039204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04315760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2231540
X-RAY DIFFRACTIONr_chiral_restr0.1180.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023304
X-RAY DIFFRACTIONr_nbd_refined0.2250.22258
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23054
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2442
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.257
X-RAY DIFFRACTIONr_mcbond_it0.8571.52687
X-RAY DIFFRACTIONr_mcangle_it1.33224248
X-RAY DIFFRACTIONr_scbond_it2.36931921
X-RAY DIFFRACTIONr_scangle_it3.5894.51702
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 281 -
Rwork0.242 5357 -
all-5638 -
obs--99.72 %

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