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- PDB-4hec: Crystal structure of a putative uncharacterized protein from Myco... -

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Basic information

Entry
Database: PDB / ID: 4hec
TitleCrystal structure of a putative uncharacterized protein from Mycobacterium tuberculosis
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / SSGCID / Mycobacterium tuberculosis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


RNA exonuclease activity / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleic acid binding / magnesium ion binding / identical protein binding
Similarity search - Function
3-5 exoribonuclease, actinobacteria / 3'-5' exoribonuclease Rv2179c-like domain / 3'-5' exoribonuclease Rv2179c-like domain / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3'-5' exoribonuclease MT2234.1 / 3'-5' exoribonuclease Rv2179c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Mycobacterium tuberculosis Rv2179c Protein Establishes a New Exoribonuclease Family with Broad Phylogenetic Distribution.
Authors: Abendroth, J. / Ollodart, A. / Andrews, E.S. / Myler, P.J. / Staker, B.L. / Edwards, T.E. / Arcus, V.L. / Grundner, C.
History
DepositionOct 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Sep 20, 2017Group: Data collection / Category: pdbx_diffrn_reflns_shell / Item: _pdbx_diffrn_reflns_shell.percent_possible_obs
Revision 1.4Feb 28, 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_ref_seq_dif / 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.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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9184
Polymers43,8692
Non-polymers492
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-24 kcal/mol
Surface area14800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.780, 76.720, 106.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein


Mass: 21934.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: MT2234.1, Rv2179c / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53513, UniProt: P9WJ73*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.99 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: EMBio JCSG+ B4: 10% PEG 8000, 8% Ethylene glycol, 100mM HEPES pH 7.5; MytuD.18400.a.A1.PS01434 at 12.8mg/ml + 2.5mM AMPPNP and MgCl2, cryo: 20% EG; the structure was solved via iodide SAD: a ...Details: EMBio JCSG+ B4: 10% PEG 8000, 8% Ethylene glycol, 100mM HEPES pH 7.5; MytuD.18400.a.A1.PS01434 at 12.8mg/ml + 2.5mM AMPPNP and MgCl2, cryo: 20% EG; the structure was solved via iodide SAD: a crystal was soaked in reservoir plus 20% ethylene glycol and 750mM NaI, anomalous amplitudes are deposited, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 31, 2012
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 396569 / Rmerge(I) obs: 0.115 / D res high: 2.4 Å / Num. obs: 26188 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
2.42.46192310010.537
2.462.53188799.410.504
2.532.6181999.910.446
2.62.68182199.810.404
2.682.77168499.910.336
2.772.87169999.910.261
2.872.98159410010.216
2.983.1157810010.171
3.13.24146410010.142
3.243.39143110010.108
3.393.58137010010.098
3.583.79127810010.085
3.794.06120299.810.077
4.064.38111710010.068
4.384.8104599.910.067
4.85.3793410010.069
5.376.281699.910.077
6.27.5969310010.073
7.5910.7354410010.057
ReflectionResolution: 1.8→50 Å / Num. all: 33216 / Num. obs: 32926 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 28.69 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 27.29
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.850.4342.4467272329196.4
1.85-1.90.4892.1768402292197.5
1.9-1.950.2235.6468282275198.4
1.95-2.010.2324.970362203199.7
2.01-2.080.1597.2171142157199.9
2.08-2.150.1359.23752521031100
2.15-2.230.14111.3480221990198.6
2.23-2.320.11415.7477621883197.4
2.32-2.430.07819.0691341873199.9
2.43-2.550.06722.6693031800199.9
2.55-2.680.05827.3949417141100
2.68-2.850.04932.731030116491100
2.85-3.040.03844.751081115121100
3.04-3.290.0352.95102781439199.9
3.29-3.60.02662.46934313281100
3.6-4.020.02474.175761188199.5
4.02-4.650.01789.975711082199.8
4.65-5.690.01788.5364189271100
5.69-8.050.01881.2949847381100
8.05-500.013102.632625444198

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.4 Å / D res low: 43.38 Å / FOM : 0.336 / FOM acentric: 0.374 / FOM centric: 0.12 / Reflection: 14132 / Reflection acentric: 12017 / Reflection centric: 2102

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
RefinementMethod to determine structure: SAD
Starting model: de novo phasing with iodide ions

Resolution: 1.8→38.39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.611 / SU ML: 0.087 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 1645 5 %RANDOM
Rwork0.1884 ---
all0.1904 33216 --
obs0.1904 31227 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.99 Å2 / Biso mean: 25.3846 Å2 / Biso min: 11.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 2 220 2792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192692
X-RAY DIFFRACTIONr_bond_other_d0.0010.022475
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9553686
X-RAY DIFFRACTIONr_angle_other_deg0.8635683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.27122.222135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82815421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9511532
X-RAY DIFFRACTIONr_chiral_restr0.0940.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02647
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 109 -
Rwork0.259 2217 -
all-2326 -
obs-2329 96.35 %
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)
11.15510.1391-0.36731.2706-0.47981.4490.04860.01470.0073-0.1098-0.04110.0195-0.0359-0.1085-0.00750.06680.0045-0.01160.01450.00260.03481.39917.08881.323
20.9015-0.1701-0.18921.2827-0.14761.36090.0159-0.1742-0.05510.1035-0.04550.02120.0455-0.05250.02960.0769-0.02780.00660.05010.00080.0418-4.3852.00199.007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 159
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B0 - 162
4X-RAY DIFFRACTION2B301

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