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- PDB-3bii: Crystal Structure of Activated MPT Synthase -

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Basic information

Entry
Database: PDB / ID: 3bii
TitleCrystal Structure of Activated MPT Synthase
Components
  • Molybdopterin-converting factor subunit 1
  • Molybdopterin-converting factor subunit 2
KeywordsTRANSFERASE / MPT synthase / Moco biosynthesis / MoaE / MoaD / ubiquitin-like / beta-hammerhead fold / Molybdenum cofactor biosynthesis
Function / homology
Function and homology information


molybdopterin synthase complex / molybdopterin adenylyltransferase complex / molybdopterin synthase activity / molybdopterin synthase / Mo-molybdopterin cofactor biosynthetic process / nucleotide binding / protein homodimerization activity / cytosol
Similarity search - Function
Molybdopterin biosynthesis MoaE subunit / Molybdopterin synthase sulfur carrier subunit / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Aldehyde Oxidoreductase; domain 3 / Beta-grasp domain ...Molybdopterin biosynthesis MoaE subunit / Molybdopterin synthase sulfur carrier subunit / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Aldehyde Oxidoreductase; domain 3 / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Molybdopterin synthase sulfur carrier subunit / Molybdopterin synthase catalytic subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsDaniels, J.N. / Schindelin, H.
Citation
Journal: Biochemistry / Year: 2008
Title: Crystal structure of a molybdopterin synthase-precursor Z complex: insight into its sulfur transfer mechanism and its role in molybdenum cofactor deficiency.
Authors: Daniels, J.N. / Wuebbens, M.M. / Rajagopalan, K.V. / Schindelin, H.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Structural studies of molybdopterin synthase provide insights into its catalytic mechanism
Authors: Rudolph, M.J. / Wuebbens, M.M. / Turque, O. / Rajagopalan, K.V. / Schindelin, H.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Molybdopterin-converting factor subunit 1
E: Molybdopterin-converting factor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7956
Polymers25,6532
Non-polymers1424
Water1,71195
1
D: Molybdopterin-converting factor subunit 1
E: Molybdopterin-converting factor subunit 2
hetero molecules

D: Molybdopterin-converting factor subunit 1
E: Molybdopterin-converting factor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,58912
Polymers51,3064
Non-polymers2848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.796, 48.735, 74.915
Angle α, β, γ (deg.)90.000, 107.770, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Molybdopterin-converting factor subunit 1 / MPT synthase subunit 1 / Molybdopterin synthase subunit 1 / Molybdenum cofactor biosynthesis ...MPT synthase subunit 1 / Molybdopterin synthase subunit 1 / Molybdenum cofactor biosynthesis protein D / Molybdopterin-converting factor small subunit


Mass: 8780.944 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: moaD, chlA4, chlM / Plasmid: pET-15b / Cell line (production host): BL21 DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30748
#2: Protein Molybdopterin-converting factor subunit 2 / MPT synthase subunit 2 / Molybdopterin synthase subunit 2 / Molybdenum cofactor biosynthesis ...MPT synthase subunit 2 / Molybdopterin synthase subunit 2 / Molybdenum cofactor biosynthesis protein E / Molybdopterin-converting factor large subunit


Mass: 16871.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: moaE, chlA5 / Plasmid: pET-15b / Cell line (production host): BL21 DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30749
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.1 Ammonium sulfate and .1M HEPES pH=7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorDate: Jan 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 9359 / % possible obs: 87.6 % / Rmerge(I) obs: 0.096 / Χ2: 1.505 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.280.3088200.67936.2
2.28-2.370.25813650.55161.8
2.37-2.480.22519280.78288.8
2.48-2.610.20621290.88996.7
2.61-2.770.19421751.16397.9
2.77-2.990.14821771.23799
2.99-3.290.11321951.72999.1
3.29-3.760.08421772.12998.8
3.76-4.740.06621922.07399
4.74-500.06922012.09399.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.891 / SU B: 20.561 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 358 4.6 %RANDOM
Rwork0.189 ---
obs0.192 7703 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.916 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.06 Å2
2--0.04 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 4 95 1899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221844
X-RAY DIFFRACTIONr_angle_refined_deg1.521.9352514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1995220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84823.62691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3115297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4311515
X-RAY DIFFRACTIONr_chiral_restr0.1020.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021417
X-RAY DIFFRACTIONr_nbd_refined0.2250.2858
X-RAY DIFFRACTIONr_nbtor_refined0.310.21216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2120
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.215
X-RAY DIFFRACTIONr_mcbond_it0.9421.51145
X-RAY DIFFRACTIONr_mcangle_it1.34921816
X-RAY DIFFRACTIONr_scbond_it1.9463803
X-RAY DIFFRACTIONr_scangle_it3.0794.5698
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 20 -
Rwork0.292 529 -
all-549 -
obs--95.64 %

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