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- PDB-1h4d: Biochemical and Structural Analysis of the Molybdenum Cofactor Bi... -

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Basic information

Entry
Database: PDB / ID: 1h4d
TitleBiochemical and Structural Analysis of the Molybdenum Cofactor Biosynthesis protein MobA
ComponentsMOLYBDOPTERIN-GUANINE DINUCLEOTIDE BIOSYNTHESIS PROTEIN A
KeywordsMOLYBDENUM COFACTOR BIOSYNTHESIS / MOLYBDOPTERIN NUCLEOTIDYL-TRANSFERASE / GTP-BINDING
Function / homology
Function and homology information


bis(molybdopterin guanine dinucleotide)molybdenum biosynthetic process / molybdenum cofactor guanylyltransferase / molybdenum cofactor guanylyltransferase activity / nucleotidyltransferase activity / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
Molybdenum cofactor guanylyltransferase / MobA-like NTP transferase / MobA-like NTP transferase domain / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / : / Molybdenum cofactor guanylyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsGuse, A. / Stevenson, C.E.M. / Kuper, J. / Buchanan, G. / Schwarz, G. / Mendel, R.R. / Lawson, D.M. / Palmer, T.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Biochemical and Structural Analysis of the Molybdenum Cofactor Biosynthesis Protein Moba
Authors: Guse, A. / Stevenson, C.E.M. / Kuper, J. / Buchanan, G. / Schwarz, G. / Giordano, G. / Magalon, A. / Mendel, R.R. / Lawson, D.M. / Palmer, T.
History
DepositionFeb 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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: MOLYBDOPTERIN-GUANINE DINUCLEOTIDE BIOSYNTHESIS PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0334
Polymers22,6421
Non-polymers3913
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.560, 41.962, 54.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2149-

HOH

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Components

#1: Protein MOLYBDOPTERIN-GUANINE DINUCLEOTIDE BIOSYNTHESIS PROTEIN A / PROTEIN FA


Mass: 22641.920 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE FULL LENGTH CONSTRUCT WAS C-TERMINALLY EXTENDED WITH A 7-RESIDUE NICKEL AFFINITY TAG OF SEQUENCE SER-HIS-HIS-HIS-HIS-HIS-HIS.
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: JM109
Description: MUTATION INTRODUCED BY 3-WAY PCR AND VERIFIED BY DNA SEQUENCING
Variant: M15[PREP4] / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / Variant (production host): M15[PREP4] / References: UniProt: P32173
#2: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Compound detailsLINKS A GUANOSINE 5'-PHOSPHATE TO MOLYDOPTERIN (MPT) FORMING MOLYBDOPTERIN GUANINE DINUCLEOTIDE ...LINKS A GUANOSINE 5'-PHOSPHATE TO MOLYDOPTERIN (MPT) FORMING MOLYBDOPTERIN GUANINE DINUCLEOTIDE (MGD). THE ENZYME EXISTS AS A MONOMER IN SOLUTION AND IS A MEMBER OF THE MOBA FAMILY OF PROTEIN. ENGINEERED MUTATION GLY 22 LEU
Sequence detailsG22L MUTANT C-TERMINAL TAG: SER-HIS-HIS-HIS-HIS-HIS-HIS

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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: 1.93 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 12 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 20% (V/V) ISOPROPANO 2% (W/V) PEG 1500, IN 100 MM CITRIC ACID ...Details: HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 12 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 20% (V/V) ISOPROPANO 2% (W/V) PEG 1500, IN 100 MM CITRIC ACID BROUGHT TO PH 5.5 WITH NAOH. CRYSTALS GROW AT 4 DEG. C AND TAKE UP TO 8 WEEK TO REACH FULL SIZE.
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Stevenson, C.E., (2000) Structure, 8, 1115.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
220 %(v/v)isopropanol1reservoir
32 %(w/v)PEG15001reservoir
4100 mMcitric acid1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 18116 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.1
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.8 / % possible all: 96.7
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E5K

1e5k


Resolution: 1.74→54.23 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.226 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.219 894 4.9 %RANDOM
Rwork0.175 ---
obs-17221 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 15.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.74→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 27 185 1648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211497
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.972047
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7415187
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_restr0.1350.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021158
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2700
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3470.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2131.5936
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11621500
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0423561
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6384.5547
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.289 54
Rwork0.222 1138
Software
*PLUS
Name: REFMAC / Version: 5.1.24 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.913
LS refinement shell
*PLUS
Highest resolution: 1.74 Å / Lowest resolution: 1.79 Å / Rfactor Rfree: 0.289 / Num. reflection Rfree: 54 / Rfactor Rwork: 0.222 / Num. reflection Rwork: 1138 / Total num. of bins used: 20

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