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- PDB-3go7: Crystal Structure of M. tuberculosis ribokinase (Rv2436) in compl... -

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Basic information

Entry
Database: PDB / ID: 3go7
TitleCrystal Structure of M. tuberculosis ribokinase (Rv2436) in complex with ribose
ComponentsRIBOKINASE RBSK
KeywordsTRANSFERASE / phosphofructokinase / carbohydrate kinase / Kinase
Function / homology
Function and homology information


ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-ribofuranose / Ribokinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsMasters, E.I. / Sun, Y. / Wang, Y. / Parker, W.B. / Li, R.
CitationJournal: To be Published
Title: Crystal structure and biochemical characterization of M.tuberculosis ribokinase (Rv2436)
Authors: Masters, E.I. / Sun, Y. / Wang, Y. / Parker, W.B. / Li, R.
History
DepositionMar 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: RIBOKINASE RBSK
B: RIBOKINASE RBSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4655
Polymers62,2662
Non-polymers1993
Water4,125229
1
A: RIBOKINASE RBSK
hetero molecules

B: RIBOKINASE RBSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4655
Polymers62,2662
Non-polymers1993
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3080 Å2
ΔGint-23 kcal/mol
Surface area21760 Å2
MethodPISA
2
A: RIBOKINASE RBSK
B: RIBOKINASE RBSK
hetero molecules

A: RIBOKINASE RBSK
B: RIBOKINASE RBSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,92910
Polymers124,5324
Non-polymers3976
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8350 Å2
ΔGint-55 kcal/mol
Surface area41340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.025, 119.207, 89.768
Angle α, β, γ (deg.)90.000, 115.000, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RIBOKINASE RBSK


Mass: 31132.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: rbsK, Rv2436 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P71913, ribokinase
#2: Sugar ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose / Ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane, 16% PEG 3350, pH 6.5, vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 9, 2008
Details: Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing. Rosenbaum-Rock vertical focusing mirror.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 26190 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Χ2: 1.197 / Net I/σ(I): 19.959
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.542.20.43811711.09189.6
2.54-2.592.60.39912650.96195.8
2.59-2.6430.38912850.93998
2.64-2.693.20.36213161.00499.5
2.69-2.753.50.30113111.03399.9
2.75-2.823.60.2713171.08100
2.82-2.893.70.23113341.129100
2.89-2.963.80.213031.164100
2.96-3.053.80.17913071.27299.8
3.05-3.153.80.13213211.298100
3.15-3.263.80.11113371.606100
3.26-3.393.80.08513071.516100
3.39-3.553.80.07413131.707100
3.55-3.733.80.06513221.8899.8
3.73-3.973.80.05813251.725100
3.97-4.273.80.05213201.13999.8
4.27-4.73.80.04113210.9399.8
4.7-5.383.80.03313330.62399.9
5.38-6.783.80.02713260.69799.9
6.78-503.70.01913560.83199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.5→42.22 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.176 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.834 / SU B: 8.147 / SU ML: 0.176 / SU R Cruickshank DPI: 0.337 / SU Rfree: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.337 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1308 5 %RANDOM
Rwork0.176 ---
obs0.179 25905 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.05 Å2 / Biso mean: 45.245 Å2 / Biso min: 22.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å20.1 Å2
2---0.18 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 12 229 4251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224092
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9615632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78723.649148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91815522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0381534
X-RAY DIFFRACTIONr_chiral_restr0.0840.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023174
X-RAY DIFFRACTIONr_nbd_refined0.2130.21963
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22847
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.213
X-RAY DIFFRACTIONr_mcbond_it0.8161.52899
X-RAY DIFFRACTIONr_mcangle_it1.45724564
X-RAY DIFFRACTIONr_scbond_it1.95431275
X-RAY DIFFRACTIONr_scangle_it3.324.51068
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 76 -
Rwork0.314 1705 -
all-1781 -
obs--92.57 %

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