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- PDB-2q5w: The X-ray Crystal Structure of Molybdopterin Synthase from Staphy... -

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Basic information

Entry
Database: PDB / ID: 2q5w
TitleThe X-ray Crystal Structure of Molybdopterin Synthase from Staphylococcus aureus
Components
  • Molybdopterin converting factor, subunit 1
  • Molybdopterin-converting factor subunit 2
KeywordsTRANSFERASE / MOLYBDOPTERIN / MOCO / MPT SYNTHASE / MOAD / MOAE / MOLYBDENUM COFACTOR BIOSYNTHESIS / beta-Grasp (ubiquitin-like) / alpha beta hammerhead fold
Function / homology
Function and homology information


molybdopterin synthase / molybdopterin synthase activity / Mo-molybdopterin cofactor biosynthetic process / nucleotide binding / cytosol
Similarity search - Function
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 ...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 converting factor, subunit 1 / Molybdopterin synthase sulfur carrier subunit
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDaniels, J.N. / Schindelin, H.
CitationJournal: 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.
History
DepositionJun 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650helix determination method: author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,4833
Polymers26,3912
Non-polymers921
Water2,720151
1
E: Molybdopterin-converting factor subunit 2
D: Molybdopterin converting factor, subunit 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)52,9666
Polymers52,7824
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)133.922, 45.754, 41.772
Angle α, β, γ (deg.)90.00, 93.36, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a heterotetramer generated by the two fold axis.

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Components

#1: 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: 17512.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: moaE / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P65401
#2: Protein Molybdopterin converting factor, subunit 1


Mass: 8878.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: moaD / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q5HDT7, UniProt: Q7A441*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 2.0 M Sodium Formate, 0.1 M Sodium Acetate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 26, 2004
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16442 / % possible obs: 94.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 29
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.065 / % possible all: 71.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT2data extraction
CBASSdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FM0

1fm0


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.848 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19321 824 5 %RANDOM
Rwork0.14866 ---
obs0.15087 15548 94.95 %-
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: 24.645 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20.23 Å2
2--2.02 Å20 Å2
3----0.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.152 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 6 151 1918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221807
X-RAY DIFFRACTIONr_bond_other_d0.0010.021634
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9472447
X-RAY DIFFRACTIONr_angle_other_deg0.8333823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7715212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47325.38591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58615326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.417157
X-RAY DIFFRACTIONr_chiral_restr0.1030.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
X-RAY DIFFRACTIONr_nbd_refined0.2170.2304
X-RAY DIFFRACTIONr_nbd_other0.1830.21624
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2883
X-RAY DIFFRACTIONr_nbtor_other0.0870.21045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1621.51395
X-RAY DIFFRACTIONr_mcbond_other0.2521.5432
X-RAY DIFFRACTIONr_mcangle_it1.30821745
X-RAY DIFFRACTIONr_scbond_it2.5983877
X-RAY DIFFRACTIONr_scangle_it3.6384.5702
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 36 -
Rwork0.154 821 -
obs--69.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.38670.8816-0.6457.4351-0.4479.63060.07060.34950.3834-0.23420.17440.6621-0.4-0.4506-0.245-0.12530.0104-0.0571-0.14080.0236-0.022129.4411.08412.238
23.95544.0108-1.5584.6134-3.981914.58230.18170.2950.5022-0.05150.15541.0432-0.5568-0.369-0.3371-0.13490.0161-0.0032-0.14250.03220.130721.4932.12814.742
311.4313-6.65787.65811.3436-1.264229.71340.51790.9909-1.1373-0.7955-0.1550.49481.34070.4661-0.3629-0.0207-0.0322-0.0276-0.0818-0.04710.012431.839-1.0098.767
43.75750.766-3.945612.51881.78615.69940.208-0.42670.13030.69530.0785-0.24480.08070.31-0.2865-0.0851-0.01360.0035-0.177-0.0217-0.095634.1243.50924.079
53.59593.1979-2.01252.9117-1.46243.16910.2066-0.07780.23390.22290.00520.33020.0092-0.0321-0.2118-0.12330.00370.0039-0.1765-0.0139-0.08831.0812.25520.708
63.179-1.21611.47020.5572-0.90782.8619-0.1412-0.0530.41790.0998-0.0055-0.1485-0.41850.19360.1467-0.1284-0.0465-0.0057-0.1239-0.0071-0.122258.86512.96224.459
72.57250.2546-0.55150.66560.70991.11750.08010.04280.0112-0.0498-0.01330.04130.2122-0.1104-0.0668-0.14320.00820.0011-0.1878-0.0237-0.143350.6936.25217.696
81.2076-0.004-0.49630.72840.31420.33810.10890.26990.129-0.12120.02470.1162-0.171-0.0272-0.1336-0.15670.00610.0177-0.09160.0154-0.148653.07614.0613.052
93.8968-1.83235.54643.7705-4.064113.00180.14470.021-0.17920.075-0.2054-0.17140.36720.27140.0606-0.184-0.00030.0289-0.13380.0076-0.1734635.09325.496
103.9310.33522.35870.7856-0.09412.47580.34550.5295-0.3321-0.2466-0.20470.12030.57190.3871-0.1408-0.07120.05340.024-0.0664-0.0481-0.137451.5783.33314.199
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1DB1 - 211 - 21
2X-RAY DIFFRACTION2DB22 - 4122 - 41
3X-RAY DIFFRACTION3DB42 - 4842 - 48
4X-RAY DIFFRACTION4DB49 - 5549 - 55
5X-RAY DIFFRACTION5DB56 - 7756 - 77
6X-RAY DIFFRACTION6EA1 - 371 - 37
7X-RAY DIFFRACTION7EA38 - 7738 - 77
8X-RAY DIFFRACTION8EA78 - 9078 - 90
9X-RAY DIFFRACTION9EA91 - 10391 - 103
10X-RAY DIFFRACTION10EA104 - 131104 - 131

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