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- PDB-3fpe: Crystal Structure of MtNAS in complex with thermonicotianamine -

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Basic information

Entry
Database: PDB / ID: 3fpe
TitleCrystal Structure of MtNAS in complex with thermonicotianamine
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 / Chem-TNA / Methyltransferase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 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

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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)68,5606
Polymers67,7012
Non-polymers8584
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-9 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.410, 68.280, 147.540
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-BR / BROMIDE ION


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


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.67 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.9792
SYNCHROTRONESRF BM30A20.98076, 0.98064, 0.97857
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDNov 19, 2007
ADSC QUANTUM 3152CCDFeb 25, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.980761
30.980641
40.978571
ReflectionResolution: 1.7→44.677 Å / Num. all: 71146 / Num. obs: 71075 / % possible obs: 98.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 5.43
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.794.80.3371.950200104180.33799.9
1.79-1.94.80.232.84758098590.2399.7
1.9-2.034.80.1594.14479492600.15999.7
2.03-2.194.80.1096.24158585910.10999.2
2.19-2.44.80.0956.83828679040.09598.8
2.4-2.694.80.087.83451371440.0898.2
2.69-3.14.80.0896.73006362880.08997.8
3.1-3.84.70.0837.12484753280.08397.3
3.8-5.384.40.054111790841110.05495.5
5.38-44.684.30.05112.4939221720.05188.4

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→39.56 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.058 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3536 5 %RANDOM
Rwork0.198 ---
obs0.2 71011 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.73 Å2 / Biso mean: 16.848 Å2 / Biso min: 5.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 50 507 4779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224354
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9815886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2275526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8223.039204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76815760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.241540
X-RAY DIFFRACTIONr_chiral_restr0.1130.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023282
X-RAY DIFFRACTIONr_nbd_refined0.2210.22072
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23034
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2372
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.236
X-RAY DIFFRACTIONr_mcbond_it0.9551.52699
X-RAY DIFFRACTIONr_mcangle_it1.45424248
X-RAY DIFFRACTIONr_scbond_it2.62331853
X-RAY DIFFRACTIONr_scangle_it4.0024.51638
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 234 -
Rwork0.257 5031 -
all-5265 -
obs--99.85 %

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