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- PDB-6b5f: Crystal structure of nicotinate mononucleotide-5,6-dimethylbenzim... -

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Basic information

Entry
Database: PDB / ID: 6b5f
TitleCrystal structure of nicotinate mononucleotide-5,6-dimethylbenzimidazole phosphoribosyltransferase CobT from Yersinia enterocolitica
ComponentsNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
KeywordsTRANSFERASE / PHOSPHORIBOSYLTRANSFERASE / 5 / 6-DIMETHYLBENZIMIDAZOLE / NICOTINATE MONONUCLEOTIDE / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / National Institute of Allergy and Infectious Diseases
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
Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
Similarity search - Component
Biological speciesYersinia enterocolitica serotype O:8 / biotype 1B
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsStogios, P.J. / Skarina, T. / McChesney, C. / Grimshaw, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: Crystal structure of nicotinate mononucleotide-5,6-dimethylbenzimidazole phosphoribosyltransferase CobT from Yersinia enterocolitica
Authors: Stogios, P.J.
History
DepositionSep 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
B: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5726
Polymers73,2532
Non-polymers3204
Water14,862825
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-70 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.155, 73.875, 119.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase / NN:DBI PRT / N(1)-alpha-phosphoribosyltransferase


Mass: 36626.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081) (bacteria)
Strain: NCTC 13174 / 8081 / Gene: cobT, YE2707 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A1JTP8, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 825 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.5, 0.2 M ammonium sulfate, 30% (w/v) PEG 5K MME, cryoprotectant paratone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 47242 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.028 / Net I/σ(I): 28.62
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 2295 / CC1/2: 0.882 / Rpim(I) all: 0.227 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_2733refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L5O

1l5o


Resolution: 1.95→24.114 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.4
RfactorNum. reflection% reflectionSelection details
Rfree0.1802 1998 4.24 %RANDOM
Rwork0.1496 ---
obs0.151 47176 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→24.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4905 0 17 825 5747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055053
X-RAY DIFFRACTIONf_angle_d0.6976854
X-RAY DIFFRACTIONf_dihedral_angle_d17.1911863
X-RAY DIFFRACTIONf_chiral_restr0.041824
X-RAY DIFFRACTIONf_plane_restr0.004895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9438-1.99240.2251320.2012967X-RAY DIFFRACTION93
1.9924-2.04620.26921310.18213190X-RAY DIFFRACTION99
2.0462-2.10640.20221400.17713186X-RAY DIFFRACTION99
2.1064-2.17430.21291420.16663175X-RAY DIFFRACTION99
2.1743-2.2520.22781450.15283227X-RAY DIFFRACTION100
2.252-2.34210.19411410.1593197X-RAY DIFFRACTION100
2.3421-2.44860.18951440.15233209X-RAY DIFFRACTION100
2.4486-2.57750.21571400.15233247X-RAY DIFFRACTION100
2.5775-2.73880.20891480.15453225X-RAY DIFFRACTION100
2.7388-2.950.17291430.14813251X-RAY DIFFRACTION100
2.95-3.24620.18611450.15273251X-RAY DIFFRACTION100
3.2462-3.71440.15791460.13343286X-RAY DIFFRACTION100
3.7144-4.67420.15451480.1263318X-RAY DIFFRACTION100
4.6742-24.1160.15961530.15853449X-RAY DIFFRACTION100
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)
15.27623.1751-2.58944.8604-1.64374.8111-0.35550.1002-0.4063-0.28030.1526-0.06590.547-0.30690.23960.20670.0431-0.01180.1912-0.02510.192523.163928.469354.4169
21.18690.5421-0.01732.31450.42781.2122-0.0546-0.079-0.0605-0.00560.0442-0.2616-0.04850.1257-0.0070.20260.01590.00170.2614-0.00090.248542.085743.960968.6415
32.2364-1.54680.16042.0204-0.55040.4799-0.00970.14080.1047-0.1725-0.0153-0.1429-0.12830.03470.04660.2737-0.02680.01610.245-0.0070.170140.731147.588454.492
41.04020.2291-0.00622.30080.18811.5686-0.0261-0.04560.0913-0.0197-0.01670.1082-0.0558-0.10530.04550.1690.0145-0.01020.20130.00170.18327.463345.752264.8481
53.96384.8073-2.81725.962-3.69874.0910.3205-0.382-0.05680.5117-0.417-0.2129-0.43340.43480.12520.1940.0323-0.00650.209-0.02590.229825.667132.790594.084
61.59990.22630.34311.12110.09951.0891-0.03770.0075-0.0179-0.0606-0.01920.0521-0.0054-0.0960.06090.23380.00460.00810.21020.0050.19647.875216.629884.1237
74.0958-1.0205-2.19584.2102-3.05224.57420.07280.21770.26490.0166-0.01920.1644-0.2622-0.2175-0.05890.2236-0.0049-0.02020.2354-0.0580.273411.304530.916386.0783
89.7414.25993.42134.19711.87294.20470.1586-0.1932-0.07970.0377-0.0823-0.06760.0964-0.0378-0.04380.2430.030.03720.1875-0.00180.162525.95528.955279.2703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -1:49)
2X-RAY DIFFRACTION2(chain A and resid 50:137)
3X-RAY DIFFRACTION3(chain A and resid 138:165)
4X-RAY DIFFRACTION4(chain A and resid 166:342)
5X-RAY DIFFRACTION5(chain B and resid 0:48)
6X-RAY DIFFRACTION6(chain B and resid 49:272)
7X-RAY DIFFRACTION7(chain B and resid 273:308)
8X-RAY DIFFRACTION8(chain B and resid 309:340)

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