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- PDB-1nvi: Orthorhombic Crystal Form of Molybdopterin Synthase -

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Basic information

Entry
Database: PDB / ID: 1nvi
TitleOrthorhombic Crystal Form of Molybdopterin Synthase
Components
  • Molybdopterin converting factor subunit 1
  • Molybdopterin converting factor subunit 2
KeywordsTRANSFERASE / Protein-Protein Complex / Molybdenum cofactor biosynthesis
Function / homology
Function and homology information


molybdopterin synthase complex / molybdopterin adenylyltransferase complex / molybdopterin synthase / molybdopterin synthase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRudolph, M.J. / Wuebbens, M.M. / Turque, O. / Rajagopalan, K.V. / Schindelin, H.
CitationJournal: 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
DepositionFeb 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)26,2267
Polymers25,7542
Non-polymers4725
Water3,567198
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)52,45314
Polymers51,5084
Non-polymers94510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area8450 Å2
ΔGint-105 kcal/mol
Surface area19790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)44.578, 94.860, 137.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11E-262-

HOH

21E-266-

HOH

DetailsThe Biological Assembly is a Heterotetramer in which Two MoaE Subunits Dimerize via a crystallographic twofold axis: -x, -y+1/2, z

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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: 8750.854 Da / Num. of mol.: 1 / Fragment: Molybdopterin Synthase - Small Subunit / Mutation: I2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MOAD OR CHLA4 OR CHLM OR B0784 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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: 17003.020 Da / Num. of mol.: 1 / Fragment: Molybdopterin Synthase - Large Subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MOAE OR CHLA5 OR B0785 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30749
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.61 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.1 M (NH4)2SO4 and 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.1 Mammonium sulfate1reservoir
20.1 MHEPES1reservoirpH7.5
315 mg/mlprotein1drop

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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: 2000 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 22162 / Num. obs: 22162 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 16.1
Reflection shellHighest resolution: 1.9 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.5 / % possible all: 82.1
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 156022
Reflection shell
*PLUS
% possible obs: 82.1 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FM0

1fm0


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.457 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20634 1138 5.1 %RANDOM
Rwork0.17509 ---
all0.17667 22062 --
obs0.17667 21024 94.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.552 Å2
Baniso -1Baniso -2Baniso -3
1-3.58 Å20 Å20 Å2
2---2.32 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 27 198 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211829
X-RAY DIFFRACTIONr_bond_other_d0.0020.021643
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9432485
X-RAY DIFFRACTIONr_angle_other_deg1.14733803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.825220
X-RAY DIFFRACTIONr_chiral_restr0.1310.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022031
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02385
X-RAY DIFFRACTIONr_nbd_refined0.1940.2350
X-RAY DIFFRACTIONr_nbd_other0.2360.21896
X-RAY DIFFRACTIONr_nbtor_other0.0850.21061
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0910.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.221
X-RAY DIFFRACTIONr_mcbond_it0.6391.51110
X-RAY DIFFRACTIONr_mcangle_it1.21321786
X-RAY DIFFRACTIONr_scbond_it1.683719
X-RAY DIFFRACTIONr_scangle_it2.8324.5699
LS refinement shellResolution: 1.901→1.951 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.33 68
Rwork0.281 1335
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)
11.05670.4240.26235.1538-0.91451.5158-0.00940.04320.0025-0.07680.0006-0.16460.03020.0930.00890.0777-0.00550.0210.0782-0.00670.05662.7716-12.079923.5148
20.8415-0.5194-0.09023.2359-0.26961.4991-0.051-0.00690.0021-0.00940.0201-0.08850.11640.08610.03080.0182-0.03050.00650.0878-0.00020.04530.463511.725414.4891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1DA1 - 811 - 81
2X-RAY DIFFRACTION2EB2 - 1502 - 150
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.35
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_plane_restr0.004
X-RAY DIFFRACTIONr_dihedral_angle_deg5.82
LS refinement shell
*PLUS
Rfactor Rfree: 0.33

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