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- PDB-5haa: Crystal structure of mpy-RNase J, an archaeal RNase J from Methan... -

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Basic information

Entry
Database: PDB / ID: 5haa
TitleCrystal structure of mpy-RNase J, an archaeal RNase J from Methanolobus psychrophilus R15
ComponentsRibonuclease J
KeywordsHYDROLASE / exoribonuclease / beta-CASP / MBL
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / RNA catabolic process / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribonuclease J, archaea / Ribonuclease J / Ribonuclease J, domain 2 / Beta-lactamase superfamily domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Biological speciesMethanolobus psychrophilus R15 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.904 Å
AuthorsFeng, N. / Li, D.F.
CitationJournal: To Be Published
Title: Molecular insights into catalysis and processive exonucleolytic mechanisms of prokaryotic RNase J revealing striking parallels with that of eukaryotic Xrn1
Authors: Zheng, X. / Feng, N. / Li, D.F. / Li, J. / Dong, X.Z.
History
DepositionDec 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn_type.id
Revision 1.2Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease J
B: Ribonuclease J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,48715
Polymers104,3612
Non-polymers1,12613
Water362
1
A: Ribonuclease J
B: Ribonuclease J
hetero molecules

A: Ribonuclease J
B: Ribonuclease J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,97430
Polymers208,7224
Non-polymers2,25226
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area15090 Å2
ΔGint-625 kcal/mol
Surface area65270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.508, 162.508, 180.659
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Ribonuclease J / RNase J


Mass: 52180.453 Da / Num. of mol.: 2 / Fragment: UNP residues 2-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanolobus psychrophilus R15 (archaea)
Gene: rnj, Mpsy_0886 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: K4MAF9, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The crystal was grown in the solution containing 2M (NH4)2SO4 and 2%-5% glycerol.
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 31664 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 39 % / Biso Wilson estimate: 92.8 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.099 / Net I/σ(I): 38.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 41.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1980refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZQ4

3zq4


Resolution: 2.904→39.033 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2737 1994 6.42 %Random selection
Rwork0.2375 ---
obs0.2399 31041 98.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.904→39.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7062 0 49 2 7113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067229
X-RAY DIFFRACTIONf_angle_d1.3059786
X-RAY DIFFRACTIONf_dihedral_angle_d16.0722687
X-RAY DIFFRACTIONf_chiral_restr0.0621115
X-RAY DIFFRACTIONf_plane_restr0.0061267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9037-2.97630.36441380.34182005X-RAY DIFFRACTION98
2.9763-3.05670.29981400.31072044X-RAY DIFFRACTION99
3.0567-3.14660.36541420.30792068X-RAY DIFFRACTION100
3.1466-3.24810.37131430.31452087X-RAY DIFFRACTION99
3.2481-3.36420.31421410.2932038X-RAY DIFFRACTION99
3.3642-3.49880.33971420.27452064X-RAY DIFFRACTION99
3.4988-3.65790.30081420.25572072X-RAY DIFFRACTION99
3.6579-3.85060.2931450.24482094X-RAY DIFFRACTION99
3.8506-4.09160.2671430.24672087X-RAY DIFFRACTION99
4.0916-4.40710.22841440.23912091X-RAY DIFFRACTION99
4.4071-4.84990.2711430.19922087X-RAY DIFFRACTION98
4.8499-5.550.25961440.22642106X-RAY DIFFRACTION99
5.55-6.98590.30691450.25592114X-RAY DIFFRACTION97
6.9859-39.03670.22021420.19262090X-RAY DIFFRACTION90
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)
15.2506-1.7703-1.26144.44881.09684.0545-0.2020.6788-0.1898-0.8588-0.1349-0.29930.03330.66640.27281.0721-0.29920.41870.9351-0.08021.0756-11.411171.9058-39.1961
23.01991.19990.37293.58220.4652.4207-0.04320.1566-0.6356-0.6220.1618-0.67230.61460.2699-0.08021.0512-0.16060.26820.7932-0.03230.9306-23.074757.3143-29.4673
32.65650.5753-1.72090.8365-0.59592.42820.2547-1.14010.1317-0.0257-0.19860.0116-0.00180.2131-0.05150.9475-0.2674-0.13941.05080.12720.8182-70.55543.958-17.832
45.5995-2.3097-1.04174.5854-1.53274.7587-0.2709-1.98870.99741.5545-0.04880.0085-0.4843-0.46940.43371.4325-0.3843-0.11581.65630.21191.1606-56.067351.64584.2803
56.9043-0.37970.00025.8475-1.38012.5848-0.3777-2.03240.16821.03660.27230.72830.0337-1.12030.31511.2365-0.4674-0.02511.86950.44841.0339-58.464546.44744.6839
63.63450.2566-0.26364.1793-0.57212.10150.0683-1.0523-0.95860.4459-0.0717-0.22841.51910.20981.4511.2579-0.455-0.14191.12780.68171.2301-49.612635.825-4.3049
74.34150.41060.46661.85210.84332.62370.5369-0.6169-0.5832-0.0668-0.2459-0.69160.64150.2822-0.11840.9158-0.2558-0.10210.97090.43311.061-32.610849.194-10.4468
83.25871.6377-0.28513.43030.07422.99270.5181-1.6468-1.56530.9153-0.1573-0.64410.43590.5043-0.06081.105-0.1947-0.251.64840.58311.3935-27.54643.7853.2988
93.68710.0658-0.2026.23971.1763.89450.0887-1.2611-0.46591.57910.2122-0.4212-0.14820.9728-0.33271.2392-0.3339-0.20681.86680.30851.1275-25.343953.71137.0807
102.72160.3905-0.17732.14551.00022.9741-0.0259-0.54240.449-0.19420.21540.0049-0.73280.34680.04070.8949-0.2814-0.10361.14050.18040.938-31.477662.1653-4.2641
112.5591-1.07850.03575.08471.47693.09010.25650.0234-0.40.0135-0.26280.27960.6991-0.68350.06560.9181-0.4987-0.15290.85350.22860.8423-58.161548.0785-18.4672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 143 )
2X-RAY DIFFRACTION2chain 'A' and (resid 144 through 447 )
3X-RAY DIFFRACTION3chain 'B' and (resid -13 through 18 )
4X-RAY DIFFRACTION4chain 'B' and (resid 19 through 52 )
5X-RAY DIFFRACTION5chain 'B' and (resid 53 through 105 )
6X-RAY DIFFRACTION6chain 'B' and (resid 106 through 198 )
7X-RAY DIFFRACTION7chain 'B' and (resid 199 through 248 )
8X-RAY DIFFRACTION8chain 'B' and (resid 249 through 282 )
9X-RAY DIFFRACTION9chain 'B' and (resid 283 through 358 )
10X-RAY DIFFRACTION10chain 'B' and (resid 359 through 390 )
11X-RAY DIFFRACTION11chain 'B' and (resid 391 through 448 )

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