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- PDB-6jbz: Structural analysis of molybdopterin synthases from two mycobacte... -

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Basic information

Entry
Database: PDB / ID: 6jbz
TitleStructural analysis of molybdopterin synthases from two mycobacteria pathogens
Components
  • MoaD/ThiS family protein
  • Molybdenum cofactor biosynthesis protein E
KeywordsTRANSFERASE / molybdopterin synthases / molybdenum cofactor biosynthesis / sulfur transfer
Function / homology
Function and homology information


molybdopterin synthase activity / molybdopterin synthase / Mo-molybdopterin cofactor biosynthetic process / nucleotide binding
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 superfamily ...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 superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Molybdopterin synthase sulfur carrier subunit / Molybdenum cofactor biosynthesis protein E
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsWang, H.Y. / Liu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaNos. 813300237 and 81520108019 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Structural analysis of molybdopterin synthases from two mycobacterial pathogens.
Authors: Wang, H. / Chen, X. / Zhang, W. / Zhou, W. / Liu, X. / Rao, Z.
History
DepositionJan 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis protein E
B: MoaD/ThiS family protein
C: Molybdenum cofactor biosynthesis protein E
D: MoaD/ThiS family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2266
Polymers49,0334
Non-polymers1922
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-63 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.076, 114.076, 121.369
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Molybdenum cofactor biosynthesis protein E / Molybdopterin synthase catalytic subunit 2


Mass: 15068.054 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: moaE2, DSI35_12490, ERS007665_01777, ERS023446_04125, ERS027644_03382, ERS027646_04529, ERS027651_03265, ERS027654_03076, ERS027656_02816, ERS027659_04568, ERS031537_04564, ERS124361_04403, ...Gene: moaE2, DSI35_12490, ERS007665_01777, ERS023446_04125, ERS027644_03382, ERS027646_04529, ERS027651_03265, ERS027654_03076, ERS027656_02816, ERS027659_04568, ERS031537_04564, ERS124361_04403, SAMEA2682864_02201, SAMEA2683035_02189
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A045HUW8, molybdopterin synthase
#2: Protein MoaD/ThiS family protein / Molybdenum cofactor biosynthesis protein D


Mass: 9448.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: moaD2, DSI35_02305, ERS007661_02601, ERS007663_03167, ERS007665_02512, ERS007672_04797, ERS007679_03857, ERS007688_03620, ERS007703_04370, ERS007720_02994, ERS007722_03637, ERS007726_00134, ...Gene: moaD2, DSI35_02305, ERS007661_02601, ERS007663_03167, ERS007665_02512, ERS007672_04797, ERS007679_03857, ERS007688_03620, ERS007703_04370, ERS007720_02994, ERS007722_03637, ERS007726_00134, ERS007739_02763, ERS007741_03204, ERS023446_04078, ERS024213_03738, ERS024276_02321, ERS027644_02085, ERS027646_03803, ERS027651_01514, ERS027652_02678, ERS027653_03930, ERS027654_04370, ERS027659_02621, ERS027661_03197, ERS027666_05139, ERS031537_04168, ERS124361_05937, SAMEA2682864_02198, SAMEA2683035_02192
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A045H6C3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 4.03 Å3/Da / Density % sol: 69.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium chloride,BIS-TRIS,Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 24895 / % possible obs: 98.8 % / Redundancy: 25 % / Biso Wilson estimate: 41.75 Å2 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.038 / Net I/σ(I): 16.8
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 24.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1993 / CC1/2: 0.96 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QIE

2qie


Resolution: 2.603→47.03 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 1269 5.12 %
Rwork0.2061 --
obs0.2084 24784 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.603→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 10 17 3349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083378
X-RAY DIFFRACTIONf_angle_d1.0484586
X-RAY DIFFRACTIONf_dihedral_angle_d14.2441180
X-RAY DIFFRACTIONf_chiral_restr0.039544
X-RAY DIFFRACTIONf_plane_restr0.004598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.603-2.70730.3611430.28752504X-RAY DIFFRACTION97
2.7073-2.83050.33891250.27312581X-RAY DIFFRACTION98
2.8305-2.97970.32551500.26312562X-RAY DIFFRACTION99
2.9797-3.16630.32141310.25422589X-RAY DIFFRACTION99
3.1663-3.41070.29891430.23692581X-RAY DIFFRACTION99
3.4107-3.75380.25271520.21112593X-RAY DIFFRACTION99
3.7538-4.29670.24061470.17932632X-RAY DIFFRACTION99
4.2967-5.41210.16781300.15572669X-RAY DIFFRACTION99
5.4121-47.03810.18961480.17572804X-RAY DIFFRACTION99

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