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- PDB-4ls9: Structure of mycobacterial nrnA homolog reveals multifunctional n... -

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Basic information

Entry
Database: PDB / ID: 4ls9
TitleStructure of mycobacterial nrnA homolog reveals multifunctional nuclease activities
ComponentsDHH family protein
KeywordsHYDROLASE / DHH-family / nanoRNase
Function / homology
Function and homology information


nucleic acid binding / metal ion binding
Similarity search - Function
inorganic pyrophosphatase (n-terminal core) / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / : / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 ...inorganic pyrophosphatase (n-terminal core) / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / : / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / DHH family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKumar, D. / Srivastav, R. / Grover, A. / Manjasetty, B.A. / Sharma, R. / Taneja, B.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Unique subunit packing in mycobacterial nanoRNase leads to alternate substrate recognitions in DHH phosphodiesterases
Authors: Srivastav, R. / Kumar, D. / Grover, A. / Singh, A. / Manjasetty, B.A. / Sharma, R. / Taneja, B.
History
DepositionJul 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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_atom_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_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_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.pdbx_leaving_atom_flag / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DHH family protein
B: DHH family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0835
Polymers71,8812
Non-polymers2023
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-29 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.870, 86.090, 66.030
Angle α, β, γ (deg.)90.00, 118.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DHH family protein


Mass: 35940.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: mc(2)155 / Gene: MSMEG_2630 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QVM9
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 6000, pH 7.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9788 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 18, 2012
RadiationMonochromator: Silicon mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.2→58.1 Å / Num. obs: 33001 / % possible obs: 99.48 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Biso Wilson estimate: 31.73 Å2
Reflection shellResolution: 2.2→2.27 Å / % possible all: 99.48

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Processing

Software
NameVersionClassification
HKL-2000data collection
Auto-Rickshawphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→34.59 Å / Cor.coef. Fo:Fc: 0.9211 / Cor.coef. Fo:Fc free: 0.8829 / Occupancy max: 1 / Occupancy min: 0.4 / SU R Cruickshank DPI: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.247 / SU Rfree Blow DPI: 0.191 / SU Rfree Cruickshank DPI: 0.194 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1666 5.07 %RANDOM
Rwork0.1761 ---
obs0.1786 32831 99.51 %-
all-32909 --
Displacement parametersBiso max: 133.3 Å2 / Biso mean: 36.83 Å2 / Biso min: 10.31 Å2
Baniso -1Baniso -2Baniso -3
1--8.9222 Å20 Å25.037 Å2
2--6.7721 Å20 Å2
3---2.15 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: LAST / Resolution: 2.2→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 8 268 4984
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1629SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes755HARMONIC5
X-RAY DIFFRACTIONt_it4893HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion652SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5885SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4893HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6696HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion17.81
LS refinement shellResolution: 2.2→2.27 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2434 163 5.46 %
Rwork0.1834 2825 -
all0.1867 2988 -
obs--99.51 %
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)
11.44811.05850.3343.13340.19481.2343-0.0662-0.03570.2272-0.0919-0.04790.0938-0.10010.02350.1142-0.10070.0174-0.0495-0.0951-0.0098-0.0007-6.84057.7349.2651
21.2824-0.0147-0.05811.8835-0.79110.77510.0214-0.17030.02740.10580.06470.25080.0182-0.1365-0.0861-0.0630.00030.0018-0.0506-0.04180.0404-19.1652-13.026952.1721
35.092-2.59532.52715.088-2.26965.00620.14850.20220.2812-0.4079-0.08670.53190.1145-0.1663-0.0618-0.10660.01280.02610.08270.04520.2471-37.9815-10.130344.843
41.38950.43710.76193.55621.22862.41490.23780.1158-0.19550.16160.0305-0.19980.59640.138-0.26820.03050.0466-0.1417-0.1325-0.01670.0128-10.9922-37.282138.8591
51.2214-0.5864-0.23412.00690.37072.0391-0.0753-0.1647-0.1484-0.04390.11270.19950.1618-0.1561-0.0374-0.10350.0038-0.0743-0.0660.00380.0736-20.0923-20.20648.6572
61.6735-1.1141.05885.0664-0.80431.719-0.1734-0.3642-0.18420.42290.25890.0695-0.1006-0.1453-0.0855-0.09080.03870.10770.18380.03620.0922-21.7147-26.46668.3758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|22 - 189}A22 - 189
2X-RAY DIFFRACTION2{A|190 - 240}A190 - 240
3X-RAY DIFFRACTION3{A|241 - 340}A241 - 340
4X-RAY DIFFRACTION4{B|22 - 189}B22 - 189
5X-RAY DIFFRACTION5{B|190 - 240}B190 - 240
6X-RAY DIFFRACTION6{B|241 - 340}B241 - 340

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