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- PDB-5mpo: Crystal structure of human molybdopterin synthase complex -

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Basic information

Entry
Database: PDB / ID: 5mpo
TitleCrystal structure of human molybdopterin synthase complex
Components
  • Molybdopterin synthase catalytic subunit
  • Molybdopterin synthase sulfur carrier subunit
KeywordsTRANSFERASE / MOCS2A / MOCS2B
Function / homology
Function and homology information


: / molybdopterin synthase / molybdopterin synthase activity / Molybdenum cofactor biosynthesis / molybdopterin cofactor biosynthetic process / Mo-molybdopterin cofactor biosynthetic process / nuclear speck / nucleotide binding / nucleoplasm / cytosol
Similarity search - Function
Molybdopterin synthase sulfur carrier subunit, eukaryote / Molybdopterin synthase catalytic subunit, eukaryotes / Molybdopterin synthase sulfur carrier subunit / Molybdopterin biosynthesis MoaE 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 ...Molybdopterin synthase sulfur carrier subunit, eukaryote / Molybdopterin synthase catalytic subunit, eukaryotes / Molybdopterin synthase sulfur carrier subunit / Molybdopterin biosynthesis MoaE 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 catalytic subunit / Molybdopterin synthase sulfur carrier subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsKopec, J. / Bailey, H. / Fitzpatrick, F. / Strain-Damerell, C. / Oberholzer, A.E. / Williams, E. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. ...Kopec, J. / Bailey, H. / Fitzpatrick, F. / Strain-Damerell, C. / Oberholzer, A.E. / Williams, E. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.
CitationJournal: To Be Published
Title: Crystal structure of human molybdopterin synthase complex
Authors: Kopec, J. / Bailey, H. / Fitzpatrick, F. / Strain-Damerell, C. / Oberholzer, A.E. / Williams, E. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.
History
DepositionDec 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Molybdopterin synthase sulfur carrier subunit
B: Molybdopterin synthase sulfur carrier subunit
C: Molybdopterin synthase catalytic subunit
D: Molybdopterin synthase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)58,1824
Polymers58,1824
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-26 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.720, 123.720, 82.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Molybdopterin synthase sulfur carrier subunit / MOCO1-A / Molybdenum cofactor synthesis protein 2 small subunit / Molybdenum cofactor synthesis ...MOCO1-A / Molybdenum cofactor synthesis protein 2 small subunit / Molybdenum cofactor synthesis protein 2A / MOCS2A / Molybdopterin-synthase small subunit / Sulfur carrier protein MOCS2A


Mass: 11838.368 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOCS2, MOCO1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O96033
#2: Protein Molybdopterin synthase catalytic subunit / MOCO1-B / Molybdenum cofactor synthesis protein 2 large subunit / Molybdenum cofactor synthesis ...MOCO1-B / Molybdenum cofactor synthesis protein 2 large subunit / Molybdenum cofactor synthesis protein 2B / MOCS2B / Molybdopterin-synthase large subunit / MPT synthase large subunit


Mass: 17252.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOCS2, MCBPE, MOCO1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O96007, molybdopterin synthase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.61 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 12% PEG3350 -- 0.1M potassium nitrate -- 0.05M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.43→61.86 Å / Num. obs: 27171 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.028 / Net I/σ(I): 15.8
Reflection shellResolution: 2.43→2.49 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.955 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.635 / Rpim(I) all: 0.472 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q5W:D, 4AP8:A

2q5w

4ap8


Resolution: 2.43→61.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.181 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.225 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 1217 4.5 %RANDOM
Rwork0.20487 ---
obs0.20718 25929 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.537 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å2-0.76 Å2-0 Å2
2---1.51 Å20 Å2
3---4.91 Å2
Refinement stepCycle: 1 / Resolution: 2.43→61.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3217 0 0 7 3224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193282
X-RAY DIFFRACTIONr_bond_other_d0.0020.023132
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9614477
X-RAY DIFFRACTIONr_angle_other_deg1.00237188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1395426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77224.677124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43915521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9781514
X-RAY DIFFRACTIONr_chiral_restr0.0990.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213682
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02680
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1086.0011716
X-RAY DIFFRACTIONr_mcbond_other5.1095.9991715
X-RAY DIFFRACTIONr_mcangle_it6.9318.9882138
X-RAY DIFFRACTIONr_mcangle_other6.9298.992139
X-RAY DIFFRACTIONr_scbond_it5.6346.3431566
X-RAY DIFFRACTIONr_scbond_other5.6326.3441567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9239.3462339
X-RAY DIFFRACTIONr_long_range_B_refined9.69947.2513422
X-RAY DIFFRACTIONr_long_range_B_other9.69747.2623423
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 76 -
Rwork0.331 1890 -
obs--100 %

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