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- PDB-3h08: Crystal structure of the Ribonuclease H1 from Chlorobium tepidum -

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Basic information

Entry
Database: PDB / ID: 3h08
TitleCrystal structure of the Ribonuclease H1 from Chlorobium tepidum
ComponentsRnh (Ribonuclease H)
KeywordsHYDROLASE / RNase H / Endonuclease / Magnesium / Metal-binding / Nuclease
Function / homology
Function and homology information


RNA catabolic process / ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / magnesium ion binding / cytoplasm
Similarity search - Function
Ribonuclease HI / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / Ribonuclease H domain / RNase H type-1 domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsRatcliff, K. / Corn, J. / Marqusee, S.
CitationJournal: Biochemistry / Year: 2009
Title: Structure, stability, and folding of ribonuclease H1 from the moderately thermophilic chlorobium tepidum: comparison with thermophilic and mesophilic homologues.
Authors: Ratcliff, K. / Corn, J. / Marqusee, S.
History
DepositionApr 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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.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 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rnh (Ribonuclease H)
B: Rnh (Ribonuclease H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7184
Polymers32,6692
Non-polymers492
Water3,927218
1
A: Rnh (Ribonuclease H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3592
Polymers16,3351
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rnh (Ribonuclease H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3592
Polymers16,3351
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.457, 33.388, 66.072
Angle α, β, γ (deg.)100.38, 99.43, 90.82
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Rnh (Ribonuclease H)


Mass: 16334.626 Da / Num. of mol.: 2 / Mutation: C33A, C63A, C133A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Gene: CT1612, rnh, rnhA / Production host: Escherichia coli (E. coli) / References: UniProt: Q93SU7, ribonuclease H
#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.: 218 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2344.84
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop7.520% PEG 4000, 0.1M sodium HEPES, 10% ispropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2982vapor diffusion, hanging drop5.426% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-111.1158
SYNCHROTRONALS 8.3.120.9794
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDMay 22, 2005
ADSC QUANTUM 315r2CCDSep 12, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si 111 KHOZU Double flat crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11581
20.97941
ReflectionResolution: 1.6→50 Å / Num. all: 36214 / Num. obs: 36214 / % possible obs: 95.5 % / Rsym value: 0.046 / Net I/σ(I): 23.3
Reflection shellResolution: 1.6→1.66 Å / Mean I/σ(I) obs: 8.3 / Rsym value: 0.093 / % possible all: 92.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0005refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.1 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.087
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19362 1758 5 %RANDOM
Rwork0.15969 ---
obs0.16146 33439 95.52 %-
all-36214 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.484 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-1.07 Å2-0.3 Å2
2--0.76 Å2-0.57 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 2 218 2495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222324
X-RAY DIFFRACTIONr_bond_other_d0.0010.022118
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9563145
X-RAY DIFFRACTIONr_angle_other_deg0.71534948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.655290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.66424.4100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94115425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6571514
X-RAY DIFFRACTIONr_chiral_restr0.090.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022569
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02451
X-RAY DIFFRACTIONr_nbd_refined0.2310.2476
X-RAY DIFFRACTIONr_nbd_other0.1940.22146
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21133
X-RAY DIFFRACTIONr_nbtor_other0.0860.21407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1870.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2110.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6771.51828
X-RAY DIFFRACTIONr_mcbond_other0.5191.5597
X-RAY DIFFRACTIONr_mcangle_it2.00122288
X-RAY DIFFRACTIONr_scbond_it3.25931077
X-RAY DIFFRACTIONr_scangle_it4.4614.5856
X-RAY DIFFRACTIONr_rigid_bond_restr1.5535442
X-RAY DIFFRACTIONr_sphericity_free8.7073220
X-RAY DIFFRACTIONr_sphericity_bonded2.44234393
LS refinement shellResolution: 1.6→1.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 92 -
Rwork0.122 2352 -
obs--92.05 %
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)
14.40670.29290.78861.3884-0.2773.81480.0084-0.20810.2377-0.00450.05630.0092-0.07780.0204-0.0647-0.14640.0167-0.0022-0.1035-0.0286-0.060811.659418.4417-26.8441
213.9462-8.068-4.84278.24382.51993.9164-0.09310.1615-0.3892-0.0151-0.00640.39680.1768-0.42830.0994-0.1585-0.0286-0.0088-0.0730.0199-0.08963.917713.8204-33.9048
33.09321.142-4.83761.1492-0.90514.2017-0.2995-0.1149-0.33720.1274-0.0418-0.11660.9034-0.45490.34130.1071-0.02050.0372-0.08150.0535-0.02713.62882.0025-21.3633
47.9163-2.10625.0283.2235-4.44228.56210.1323-0.6903-0.20690.1145-0.00220.2060.3275-0.358-0.13-0.08550.00040.04310.04720.0261-0.06943.346210.0066-18.0204
526.9641-9.0854-6.07137.40381.23596.2186-0.26890.6043-0.689-0.187-0.0160.1510.4846-0.16140.2849-0.0684-0.03760.01-0.1180.0023-0.0636.27098.2544-33.4507
65.12152.81464.35714.06432.514514.4149-0.05720.28740.1933-0.15540.3215-0.3035-0.42010.4636-0.2643-0.15320.01320.03710.0098-0.02640.008921.320819.1893-30.9453
71.91520.19340.70675.2828-0.86573.80350.0296-0.0313-0.0309-0.17650.0193-0.1212-0.06030.062-0.0489-0.10690.01830.0327-0.1469-0.0011-0.09232.5298-5.26347.0869
812.0126-14.1028-0.201324.61623.13154.54080.1419-0.2639-0.23420.04870.0220.35280.5031-0.3389-0.164-0.0835-0.0509-0.0245-0.1210.0323-0.0745-1.5833-13.457214.084
90.87851.2820.75523.2911.93215.5888-0.03280.01030.0064-0.4635-0.16680.41260.1162-0.89020.19960.0153-0.0067-0.07120.0196-0.0319-0.0229-10.7479-13.4314-0.3492
1011.3656-14.5889-3.000930.73296.82926.0412-0.0919-0.6084-0.01760.91840.02610.58890.1521-0.45150.0658-0.0959-0.0741-0.0137-0.0006-0.039-0.0052-7.32-10.263514.0368
112.28281.3393-1.52874.5717-4.965118.69710.1694-0.10960.28110.02970.0258-0.0097-0.5304-0.069-0.19520.01050.02260.0464-0.1795-0.0193-0.0693.2514.589311.3237
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 61
2X-RAY DIFFRACTION2A62 - 70
3X-RAY DIFFRACTION3A71 - 92
4X-RAY DIFFRACTION4A97 - 115
5X-RAY DIFFRACTION5A116 - 123
6X-RAY DIFFRACTION6A126 - 145
7X-RAY DIFFRACTION7B2 - 61
8X-RAY DIFFRACTION8B62 - 70
9X-RAY DIFFRACTION9B71 - 115
10X-RAY DIFFRACTION10B116 - 124
11X-RAY DIFFRACTION11B125 - 145

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