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- PDB-1e5k: CRYSTAL STRUCTURE OF THE MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN... -

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Basic information

Entry
Database: PDB / ID: 1e5k
TitleCRYSTAL STRUCTURE OF THE MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN MOBA (PROTEIN FA) FROM ESCHERICHIA COLI AT NEAR ATOMIC RESOLUTION
ComponentsMOLYBDOPTERIN-GUANINE DINUCLEOTIDE BIOSYNTHESIS PROTEIN A
KeywordsMOLYBDOPTERIN NUCLEOTIDYL-TRANSFERASE
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 / MAD / Resolution: 1.35 Å
AuthorsStevenson, C.E.M. / Sargent, F. / Buchanan, G. / Palmer, T. / Lawson, D.M.
CitationJournal: Structure / Year: 2000
Title: Crystal Structure of the Molybdenum Cofactor Biosynthesis Protein Moba from Escherichia Coli at Near Atomic Resolution
Authors: Stevenson, C.E.M. / Sargent, F. / Buchanan, G. / Palmer, T. / Lawson, D.M.
History
DepositionJul 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2000Provider: 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 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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Assembly

Deposited unit
A: MOLYBDOPTERIN-GUANINE DINUCLEOTIDE BIOSYNTHESIS PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9774
Polymers22,5861
Non-polymers3913
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.574, 41.758, 54.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 22585.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE WILD-TYPE 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: K12 / Cellular location: CYTOPLASM / Gene: MOBA / Plasmid: PKK223-3 / Cellular location (production host): CYTOPLASM / Gene (production host): MOBA / 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.: 149 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: BIOSYNTHESIS OF MOLYBDOPTERIN GUANINE DINUCLEOTIDE. SEEMS TO BE INVOLVED IN THE ...FUNCTION: BIOSYNTHESIS OF MOLYBDOPTERIN GUANINE DINUCLEOTIDE. SEEMS TO BE INVOLVED IN THE ATTACHMENT OF GMP TO MOLYBDOPTERIN. PATHWAY: MOLYBDENUM COFACTOR BIOSYNTHESIS.
Sequence detailsC-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) ISOPROPANOL, 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) ISOPROPANOL, 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 WEEKS TO REACH FULL SIZE.
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
220 %(v/v)isopropanol1reservoir
32 %(w/v)PEG15001reservoir
4100 mMcitric acid1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Feb 15, 2000 / Details: MIRRORS
RadiationMonochromator: DIAMOND C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.35→40 Å / Num. obs: 38263 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 6.9
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 5.2 / % possible all: 83.4
Reflection shell
*PLUS
% possible obs: 83.4 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.06
Details: ANISOTROPIC THERMAL PARAMETER REFINEMENT WAS USED FOR LAST CYCLE. RESIDUES 15 A TO 21 A WERE POORLY DEFINED IN ELECTRON DENSITY MAPS. ALL LARGE SIDE-CHAINS IN THIS REGION WERE TRUNCATED TO ALA.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1921 5 %RANDOM
Rwork0.184 ---
obs-38263 97.9 %-
Displacement parametersBiso mean: 21.7 Å2
Refinement stepCycle: LAST / Resolution: 1.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 27 149 1599
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.2993
X-RAY DIFFRACTIONp_mcangle_it3.0735
X-RAY DIFFRACTIONp_scbond_it3.3716
X-RAY DIFFRACTIONp_scangle_it4.3338
X-RAY DIFFRACTIONp_plane_restr0.03230.04
X-RAY DIFFRACTIONp_chiral_restr0.1060.15
X-RAY DIFFRACTIONp_singtor_nbd0.1730.3
X-RAY DIFFRACTIONp_multtor_nbd0.2570.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.87
X-RAY DIFFRACTIONp_staggered_tor13.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor19.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

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