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- PDB-1tv8: Structure of MoaA in complex with S-adenosylmethionine -

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Basic information

Entry
Database: PDB / ID: 1tv8
TitleStructure of MoaA in complex with S-adenosylmethionine
ComponentsMolybdenum cofactor biosynthesis protein A
KeywordsLIGAND BINDING PROTEIN / TIM barrel
Function / homology
Function and homology information


GTP 3',8-cyclase / GTP 3',8'-cyclase activity / Mo-molybdopterin cofactor biosynthetic process / S-adenosyl-L-methionine binding / 4 iron, 4 sulfur cluster binding / GTP binding / metal ion binding
Similarity search - Function
Molybdenum cofactor synthesis C-terminal / Molybdenum cofactor biosynthesis protein A / : / Molybdenum Cofactor Synthesis C / MoaA/NifB/PqqE, iron-sulphur binding, conserved site / moaA / nifB / pqqE family signature. / : / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily ...Molybdenum cofactor synthesis C-terminal / Molybdenum cofactor biosynthesis protein A / : / Molybdenum Cofactor Synthesis C / MoaA/NifB/PqqE, iron-sulphur binding, conserved site / moaA / nifB / pqqE family signature. / : / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / GTP 3',8-cyclase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsHaenzelmann, P. / Schindelin, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans.
Authors: Hanzelmann, P. / Schindelin, H.
History
DepositionJun 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis protein A
B: Molybdenum cofactor biosynthesis protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,81111
Polymers78,2622
Non-polymers2,5509
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-138 kcal/mol
Surface area28150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.982, 103.305, 189.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLUGLUAA3 - 3293 - 329
2GLNGLNBB4 - 3294 - 329
DetailsThe biological assembly is a dimer

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Molybdenum cofactor biosynthesis protein A / moaA


Mass: 39130.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 or MW2 / Gene: moaA / Production host: Escherichia coli (E. coli) / References: UniProt: P65388

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Non-polymers , 5 types, 137 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.9 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Na formate, HEPES, DMSO, DTT, S-adenosylemthionine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Apr 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 47193
Reflection shellResolution: 2.2→2.24 Å / % possible all: 84.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
FFTmodel building
REFMAC5.1.24refinement
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→95.35 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.651 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24113 2399 5.1 %RANDOM
Rwork0.21275 ---
obs0.21423 44700 96.7 %-
all-44700 --
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: 40.807 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--2.15 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.2→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5273 0 104 128 5505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225480
X-RAY DIFFRACTIONr_bond_other_d0.0050.024946
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.9837412
X-RAY DIFFRACTIONr_angle_other_deg0.93311517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9325651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025969
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021111
X-RAY DIFFRACTIONr_nbd_refined0.2170.21167
X-RAY DIFFRACTIONr_nbd_other0.2420.25864
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.23305
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2158
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8011.53245
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51225252
X-RAY DIFFRACTIONr_scbond_it2.46332235
X-RAY DIFFRACTIONr_scangle_it4.1294.52112
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Ens-ID: 1 / Number: 5147 / Refine-ID: X-RAY DIFFRACTION

Dom-IDTypeRms dev position (Å)Weight position
1medium positional0.480.5
2medium thermal0.932
LS refinement shellResolution: 2.205→2.262 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.4 143
Rwork0.442 2731
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)
12.45090.38160.8591.28480.19462.88650.1824-0.178-0.33770.14290.0104-0.06720.39110.0036-0.19280.0097-0.0115-0.03150.27520.01960.129922.72270.25916.191
21.35170.08920.03042.4489-2.06692.8933-0.05310.0247-0.03370.0126-0.3124-0.3309-0.15820.57320.36540.1520.01420.00020.66450.23980.278234.45451.98948.966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 3293 - 329
2X-RAY DIFFRACTION2BB4 - 3294 - 329

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