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- PDB-4hdr: Crystal Structure of ArsAB in Complex with 5,6-dimethylbenzimidazole -

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Basic information

Entry
Database: PDB / ID: 4hdr
TitleCrystal Structure of ArsAB in Complex with 5,6-dimethylbenzimidazole
Components
  • ArsA
  • ArsB
KeywordsTRANSFERASE
Function / homology
Function and homology information


nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity / cobalamin biosynthetic process
Similarity search - Function
5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1 / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, bacterial type / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, N-terminal / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain / Phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily / Rossmann fold / Orthogonal Bundle ...5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1 / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, bacterial type / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, N-terminal / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain / Phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5,6-DIMETHYLBENZIMIDAZOLE / Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase / Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
Similarity search - Component
Biological speciesSporomusa ovata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsNewmister, S.A. / Chan, C.H. / Escalante-Semerena, J.C. / Rayment, I.
CitationJournal: Biochemistry / Year: 2012
Title: Structural Insights into the Function of the Nicotinate Mononucleotide:phenol/p-cresol Phosphoribosyltransferase (ArsAB) Enzyme from Sporomusa ovata.
Authors: Newmister, S.A. / Chan, C.H. / Escalante-Semerena, J.C. / Rayment, I.
History
DepositionOct 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ArsA
B: ArsB
C: ArsA
D: ArsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,18319
Polymers145,0844
Non-polymers1,09915
Water21,4561191
1
A: ArsA
B: ArsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0609
Polymers72,5422
Non-polymers5197
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-6 kcal/mol
Surface area23690 Å2
MethodPISA
2
C: ArsA
D: ArsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,12310
Polymers72,5422
Non-polymers5818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint5 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.727, 77.393, 152.269
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the ArsAB heterodimer.

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Components

#1: Protein ArsA


Mass: 36323.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporomusa ovata (bacteria) / Gene: arsA / Plasmid: pARSAB22 / Production host: Escherichia coli (E. coli) / Strain (production host): JE13607
References: UniProt: F6MZ55, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
#2: Protein ArsB


Mass: 36218.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporomusa ovata (bacteria) / Gene: arsB / Plasmid: pARSAB22 / Production host: Escherichia coli (E. coli) / Strain (production host): JE13607
References: UniProt: F6MZ56, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
#3: Chemical ChemComp-DMD / 5,6-DIMETHYLBENZIMIDAZOLE


Mass: 146.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10N2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1191 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 298 K / pH: 7.1
Details: 12.5% MEPEG5K, 100 mM MOPS pH 7.1 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 11, 2011
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 211213 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 23.2
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.229 / % possible all: 95.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.258 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
RfactorNum. reflection% reflectionSelection details
Rfree0.219 10597 5 %RANDOM
Rwork0.186 ---
obs0.188 211073 97.3 %-
all-221670 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å2-0 Å2-0.01 Å2
2--0.22 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9599 0 74 1191 10864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.01910134
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.451.98313790
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3951414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02124.354356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.125151728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5911562
X-RAY DIFFRACTIONr_chiral_restr0.1580.21674
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217458
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 770 -
Rwork0.255 14220 -
obs--94.6 %

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