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- PDB-1fma: MOLYBDOPTERIN SYNTHASE (MOAD/MOAE) -

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Basic information

Entry
Database: PDB / ID: 1fma
TitleMOLYBDOPTERIN SYNTHASE (MOAD/MOAE)
Components
  • MOLYBDOPTERIN CONVERTING FACTOR, SUBUNIT 1
  • MOLYBDOPTERIN CONVERTING FACTOR, SUBUNIT 2
KeywordsTRANSFERASE / Isopeptide bond / 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: 1.58 Å
AuthorsRudolph, M.J. / Wuebbens, M.M. / Rajagolpalan, K.V. / Schindelin, H.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of molybdopterin synthase and its evolutionary relationship to ubiquitin activation.
Authors: Rudolph, M.J. / Wuebbens, M.M. / Rajagopalan, K.V. / Schindelin, H.
History
DepositionAug 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Jun 16, 2021Group: Advisory / Derived calculations / Category: pdbx_distant_solvent_atoms / struct_site
Item: _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)25,8745
Polymers25,7682
Non-polymers1063
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-33 kcal/mol
Surface area10920 Å2
MethodPISA
2
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)51,74910
Polymers51,5364
Non-polymers2136
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7190 Å2
ΔGint-87 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.150, 47.959, 74.146
Angle α, β, γ (deg.)90.00, 107.35, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a heteroteteramer consisting of two alpha subunits and two beta subunits where the alpha-beta heterodimer falls on a crystallographic twofold axis of symmetry to generate the heterotetramer

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Components

#1: Protein MOLYBDOPTERIN CONVERTING FACTOR, SUBUNIT 1


Mass: 8764.880 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P30748
#2: Protein MOLYBDOPTERIN CONVERTING FACTOR, SUBUNIT 2


Mass: 17003.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P30749
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: Sodium chloride, Hepes , pH 7.5, VAPOR DIFFUSION, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 M1reservoirNaCl
20.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.58→20 Å / Num. all: 150077 / Num. obs: 29821 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 19.32 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.5
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 5 % / Rmerge(I) obs: 0.294 / % possible all: 95.2
Reflection
*PLUS
Num. measured all: 150077
Reflection shell
*PLUS
% possible obs: 88.7 % / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.58→20 Å / SU B: 2.66084 / SU ML: 0.09354 / σ(F): 0 / ESU R: 0.16872 / ESU R Free: 0.14205 / Stereochemistry target values: Murshudov
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1349 4.9 %RANDOM
Rwork0.172 ---
obs0.1734 25945 95.2 %-
all-27242 --
Displacement parametersBiso mean: 20.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0.33 Å2
2---0.06 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 3 178 1939
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0280.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.2161.927
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.4371.5
X-RAY DIFFRACTIONp_mcangle_it3.6672
X-RAY DIFFRACTIONp_scbond_it5.0583
X-RAY DIFFRACTIONp_scangle_it7.5034.5
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1620.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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