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- PDB-3hst: N-Terminal RNASE H domain of rv2228c from mycobacterium tuberculo... -

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Basic information

Entry
Database: PDB / ID: 3hst
TitleN-Terminal RNASE H domain of rv2228c from mycobacterium tuberculosis as a fusion protein with maltose binding protein
Components
  • Maltose-binding periplasmic protein
  • Protein Rv2228c/MT2287
KeywordsHYDROLASE / Ribonuclease H1 / RV2228C n-terminal domain / mycobacterium / tuberculosis / fusion protein / maltose binding protein
Function / homology
Function and homology information


double-stranded RNA-specific ribonuclease activity / adenosylcobalamin/alpha-ribazole phosphatase / alpha-ribazole phosphatase activity / DNA/RNA hybrid binding / cobalamin biosynthetic process / RNA catabolic process / ribonuclease H / detection of maltose stimulus / maltose binding / maltose transport complex ...double-stranded RNA-specific ribonuclease activity / adenosylcobalamin/alpha-ribazole phosphatase / alpha-ribazole phosphatase activity / DNA/RNA hybrid binding / cobalamin biosynthetic process / RNA catabolic process / ribonuclease H / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / RNA-DNA hybrid ribonuclease activity / outer membrane-bounded periplasmic space / nucleic acid binding / periplasmic space / DNA damage response / membrane / metal ion binding
Similarity search - Function
RNase H, phosphoglycerate mutase domain-containing / Reverse transcriptase-like / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein ...RNase H, phosphoglycerate mutase domain-containing / Reverse transcriptase-like / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Ribonuclease H-like superfamily/Ribonuclease H / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Ribonuclease H domain / RNase H type-1 domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltotriose / D(-)-TARTARIC ACID / Maltose/maltodextrin-binding periplasmic protein / Uncharacterized protein MT2287 / Bifunctional protein Rv2228c
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWatkins, H.A. / Baker, E.N.
CitationJournal: J.Bacteriol. / Year: 2010
Title: Structural and functional characterization of an RNase HI domain from the bifunctional protein Rv2228c from Mycobacterium tuberculosis.
Authors: Watkins, H.A. / Baker, E.N.
History
DepositionJun 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein
B: Protein Rv2228c/MT2287
C: Maltose-binding periplasmic protein
D: Protein Rv2228c/MT2287
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,51710
Polymers115,1714
Non-polymers1,3456
Water5,495305
1
A: Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0933
Polymers42,5271
Non-polymers5672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein Rv2228c/MT2287


Theoretical massNumber of molelcules
Total (without water)15,0591
Polymers15,0591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3055
Polymers42,5271
Non-polymers7794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein Rv2228c/MT2287


Theoretical massNumber of molelcules
Total (without water)15,0591
Polymers15,0591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.632, 101.383, 76.091
Angle α, β, γ (deg.)90.00, 109.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSSERSERAA14 - 3777 - 370
21LYSLYSSERSERCC14 - 3777 - 370
12VALVALMETMETBB1 - 1302 - 131
22VALVALMETMETDD1 - 1302 - 131

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Maltose-binding periplasmic protein / MMBP / Maltodextrin-binding protein


Mass: 42526.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: b4034, JW3994, malE, Maltose Binding Protein / Plasmid: pMAL-C2x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9
#2: Protein Protein Rv2228c/MT2287


Mass: 15058.917 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT2287, MTCY427.09c, Rv2228c / Plasmid: pMAL-C2x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P64955, UniProt: P9WLH5*PLUS, Hydrolases

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Sugars , 1 types, 2 molecules

#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 309 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG2000, 0.2M Ammounium tartrate, pH pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
PH range: pH7.5

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98397 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98397 Å / Relative weight: 1
ReflectionResolution: 2.25→41.45 Å / Num. obs: 50220 / % possible obs: 100 %
Reflection shellResolution: 2.25→2.37 Å / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 11.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
PHASERphasing
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→41.45 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.289 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23854 2576 5.1 %RANDOM
Rwork0.18265 ---
obs0.18549 47622 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.324 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å2-2.31 Å2
2--0.44 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.25→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7732 0 90 305 8127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0228035
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.96810912
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97551007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54925.402348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.414151315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8011528
X-RAY DIFFRACTIONr_chiral_restr0.1250.21214
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026064
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.23796
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.25473
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2439
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3520.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0251.55180
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56528018
X-RAY DIFFRACTIONr_scbond_it2.83833355
X-RAY DIFFRACTIONr_scangle_it4.2854.52894
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2799medium positional0.340.5
2B991medium positional0.350.5
1A2799medium thermal1.142
2B991medium thermal1.352
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 184 -
Rwork0.212 3534 -
obs--100 %
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)
10.54670.16210.30151.01180.43250.63920.0336-0.0880.02980.0069-0.05110.05580.0459-0.13260.01750.0415-0.0240.00280.1392-0.00360.0612-5.6165-0.291527.1419
21.7022-0.1538-0.16381.66440.33632.24550.07440.01860.0153-0.03-0.03870.0410.1937-0.0879-0.03570.0819-0.0342-0.02410.06560.00930.0046-14.6488-11.4451-9.135
33.07070.30710.70942.30195.015414.86440.26-0.0322-0.0701-0.1018-0.1745-0.0267-0.4318-0.8274-0.08560.10320.0072-0.04590.05620.03020.057-23.5144-12.7424-12.7005
421.1137-4.76660.29565.1042-0.02320.72550.41170.7942-0.1801-0.1314-0.4194-0.45950.12630.15580.00780.104-0.0516-0.03310.03780.0149-0.0426-5.4907-14.2241-23.4535
50.5309-0.11710.03590.9922-0.02570.41770.02060.03160.0227-0.063-0.0284-0.0141-0.0147-0.03110.00780.05220.0012-0.01720.0940.0090.076727.3662-4.294518.8655
61.3160.6702-0.31192.69550.30520.8582-0.13670.07340.053-0.10780.1624-0.2740.04760.0746-0.02570.04340.0044-0.02140.07560.01230.0951-1.24965.8075-17.3697
73.74220.77040.26194.4279-0.18075.5378-0.07930.02460.1932-0.09470.0966-0.513-0.10460.0787-0.01730.11790.0109-0.07470.09150.00220.26414.08338.7316-14.137
820.9841-13.68972.822625.3642-3.19254.1494-1.046-0.7046-0.30520.71631.06081.1887-0.0952-0.774-0.01480.1884-0.0092-0.1030.12480.07270.0579-15.55338.6254-21.3283
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 378
2X-RAY DIFFRACTION2B0 - 106
3X-RAY DIFFRACTION3B107 - 119
4X-RAY DIFFRACTION4B122 - 138
5X-RAY DIFFRACTION5C10 - 378
6X-RAY DIFFRACTION6D1 - 85
7X-RAY DIFFRACTION7D86 - 121
8X-RAY DIFFRACTION8D122 - 131

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