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- PDB-1nz0: RNASE P PROTEIN FROM THERMOTOGA MARITIMA -

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Basic information

Entry
Database: PDB / ID: 1nz0
TitleRNASE P PROTEIN FROM THERMOTOGA MARITIMA
ComponentsRibonuclease P protein component
KeywordsHYDROLASE / ENDONUCLEASE / RNASE / ALFA-BETA SANDWICH / DIMER / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


3'-tRNA processing endoribonuclease activity / ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / tRNA binding
Similarity search - Function
Ribonuclease P / Ribonuclease P, conserved site / Ribonuclease P / Bacterial ribonuclease P protein component signature. / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonuclease P protein component
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å
AuthorsKazantsev, A.V. / Krivenko, A.A. / Harrington, D.J. / Carter, R.J. / Holbrook, S.R. / Adams, P.D. / Pace, N.R. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: High-resolution structure of RNase P protein from Thermotoga maritima.
Authors: Kazantsev, A.V. / Krivenko, A.A. / Harrington, D.J. / Carter, R.J. / Holbrook, S.R. / Adams, P.D. / Pace, N.R.
History
DepositionFeb 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Ribonuclease P protein component
C: Ribonuclease P protein component
B: Ribonuclease P protein component
D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,24920
Polymers57,7124
Non-polymers1,53716
Water9,602533
1
A: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6203
Polymers14,4281
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7164
Polymers14,4281
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0047
Polymers14,4281
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9086
Polymers14,4281
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Ribonuclease P protein component
hetero molecules

A: Ribonuclease P protein component
hetero molecules

C: Ribonuclease P protein component
hetero molecules

D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,24920
Polymers57,7124
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
crystal symmetry operation2_747-x+2,y-1/2,-z+21
Buried area5710 Å2
ΔGint-205 kcal/mol
Surface area23950 Å2
MethodPISA
6
B: Ribonuclease P protein component
hetero molecules

C: Ribonuclease P protein component
hetero molecules

A: Ribonuclease P protein component
D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,24920
Polymers57,7124
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-207 kcal/mol
Surface area23750 Å2
MethodPISA
7
A: Ribonuclease P protein component
C: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3367
Polymers28,8562
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-74 kcal/mol
Surface area11650 Å2
MethodPISA
8
B: Ribonuclease P protein component
D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,91313
Polymers28,8562
Non-polymers1,05711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-139 kcal/mol
Surface area12430 Å2
MethodPISA
9
B: Ribonuclease P protein component
hetero molecules

D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,91313
Polymers28,8562
Non-polymers1,05711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2680 Å2
ΔGint-133 kcal/mol
Surface area12960 Å2
MethodPISA
10
C: Ribonuclease P protein component
hetero molecules

A: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3367
Polymers28,8562
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area1800 Å2
ΔGint-65 kcal/mol
Surface area12220 Å2
MethodPISA
11
B: Ribonuclease P protein component
hetero molecules

D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,91313
Polymers28,8562
Non-polymers1,05711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_747-x+2,y-1/2,-z+21
Buried area2430 Å2
ΔGint-133 kcal/mol
Surface area13210 Å2
MethodPISA
12
B: Ribonuclease P protein component
hetero molecules

D: Ribonuclease P protein component
hetero molecules

C: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,62917
Polymers43,2843
Non-polymers1,34514
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
Buried area4600 Å2
ΔGint-176 kcal/mol
Surface area17990 Å2
MethodPISA
13
B: Ribonuclease P protein component
hetero molecules

C: Ribonuclease P protein component
hetero molecules

D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,62917
Polymers43,2843
Non-polymers1,34514
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
crystal symmetry operation2_747-x+2,y-1/2,-z+21
Buried area3970 Å2
ΔGint-173 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.227, 64.143, 68.326
Angle α, β, γ (deg.)90.00, 102.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribonuclease P protein component / / RNaseP protein / RNase P protein / Protein C5


Mass: 14427.935 Da / Num. of mol.: 4 / Mutation: M1S, L41M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: RNPA OR TM1463 / Plasmid: PGEX4TA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: Q9X1H4, ribonuclease P
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.28 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 1500, potassium sulfate, sodium acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion / PH range low: 5.2 / PH range high: 4.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mM1reservoirpH4.8-5.2NaOAc
212-18 %PEG15001reservoir
3200 mM1reservoirK2SO4
43 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9792 / Wavelength: 0.9792 Å
DetectorType: ADSC / Detector: CCD / Date: May 11, 2001 / Details: W16 WIGGLER
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 118678 / Num. obs: 118678 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 6.53 % / Biso Wilson estimate: 13.688 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 5.3
Reflection shellResolution: 1.2→1.35 Å / Redundancy: 4.01 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 1.1 / Num. unique all: 16982 / Rsym value: 0.565 / % possible all: 38.7
Reflection
*PLUS
Num. measured all: 774818
Reflection shell
*PLUS
% possible obs: 38.7 % / Num. unique obs: 16982 / Num. measured obs: 67203

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXmodel building
SHELXL-97refinement
CCP4(SCALA)data scaling
CNSphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.2→30 Å / Num. parameters: 41196 / Num. restraintsaints: 57603 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.14%
RfactorNum. reflection% reflectionSelection details
Rfree0.217 5799 4.9 %RANDOM
Rwork0.1625 ---
all0.1634 118678 --
obs0.1625 117875 79.6 %-
Refine analyzeNum. disordered residues: 148 / Occupancy sum hydrogen: 3913 / Occupancy sum non hydrogen: 4230.3
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 80 533 4577
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0.009
X-RAY DIFFRACTIONs_from_restr_planes0.0287
X-RAY DIFFRACTIONs_zero_chiral_vol0.134
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.141
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.076
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rwork: 0.1634
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.715
X-RAY DIFFRACTIONs_plane_restr0.029
X-RAY DIFFRACTIONs_chiral_restr0.134

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