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- PDB-1frw: STRUCTURE OF E. COLI MOBA WITH BOUND GTP AND MANGANESE -

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Basic information

Entry
Database: PDB / ID: 1frw
TitleSTRUCTURE OF E. COLI MOBA WITH BOUND GTP AND MANGANESE
ComponentsMOLYBDOPTERIN-GUANINE DINUCLEOTIDE BIOSYNTHESIS PROTEIN
KeywordsMETAL BINDING PROTEIN / Molybdenum cofactor (Moco) / Moco Biosynthesis / Molybdopterin (MPT) / Molybdopterin Guanine Dinucleotide (MGD)
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
ACETATE ION / GUANOSINE-5'-TRIPHOSPHATE / : / Molybdenum cofactor guanylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsLake, M.W. / Temple, C.A. / Rajagopalan, K.V. / Schindelin, H.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The crystal structure of the Escherichia coli MobA protein provides insight into molybdopterin guanine dinucleotide biosynthesis.
Authors: Lake, M.W. / Temple, C.A. / Rajagopalan, K.V. / Schindelin, H.
History
DepositionSep 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr1_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3725
Polymers21,6701
Non-polymers7034
Water3,027168
1
A: MOLYBDOPTERIN-GUANINE DINUCLEOTIDE BIOSYNTHESIS PROTEIN
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)178,97940
Polymers173,3598
Non-polymers5,62132
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area24370 Å2
ΔGint-656 kcal/mol
Surface area54970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.387, 124.387, 67.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Cell settingtetragonal
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-196-

ZN

DetailsThe biological assembly is an octamer constructed from chain A. The octamer has 42 symmetry and is entirely generated by crystallographic symmetry operations in the I422 tetragonal space group. His 49 from 2 different monomers along with 2 acetate ligands coordinate a zinc atom at the dimer interface.

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 21669.854 Da / Num. of mol.: 1 / Fragment: MOBA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PCT800A / Production host: Escherichia coli (E. coli) / References: UniProt: P32173

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Non-polymers , 5 types, 172 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlenzyme1drop
22.5-3 Msodium acetate1reservoir
30.1 Mcacodylic acid1reservoirpH6.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 26350 / Num. obs: 26350 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14
Reflection shellResolution: 1.75→1.83 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.441 / Num. unique all: 2895 / % possible all: 100
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 100 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.75→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Refmac dictionary / Details: Hydrogens have been added in the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1330 5.1 %RANDOM
Rwork0.1834 ---
all0.1856 25861 --
obs0.1856 24531 96.2 %-
Solvent computationSolvent model: Babinet's principle
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 38 168 1652
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.021
X-RAY DIFFRACTIONp_angle_d2.241.972
X-RAY DIFFRACTIONp_angle_deg2.241.972
X-RAY DIFFRACTIONp_planar_d0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.1230.2
X-RAY DIFFRACTIONp_mcbond_it2.3051.5
X-RAY DIFFRACTIONp_mcangle_it3.6952
X-RAY DIFFRACTIONp_scbond_it5.3213
X-RAY DIFFRACTIONp_scangle_it8.124.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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