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- PDB-3b4t: Crystal structure of Mycobacterium tuberculosis RNase PH, the Myc... -

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Basic information

Entry
Database: PDB / ID: 3b4t
TitleCrystal structure of Mycobacterium tuberculosis RNase PH, the Mycobacterium tuberculosis Structural Genomics Consortium target Rv1340
ComponentsRibonuclease PH
KeywordsTRANSFERASE / RNase / tRNA nucleotidyltransferase / ribonuclease / RPHA / Structural Genomics / TBSGC / Mycobacterium tuberculosis Structural Genomics Consortium / tRNA processing / TB Structural Genomics Consortium / PSI / Protein Structure Initiative
Function / homology
Function and homology information


tRNA nucleotidyltransferase / tRNA nucleotidyltransferase activity / rRNA catabolic process / tRNA processing / rRNA processing / 3'-5'-RNA exonuclease activity / tRNA binding / plasma membrane
Similarity search - Function
Ribonuclease PH, bacterial-type / Ribonuclease PH, conserved site / Ribonuclease PH signature. / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 ...Ribonuclease PH, bacterial-type / Ribonuclease PH, conserved site / Ribonuclease PH signature. / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ribonuclease PH / Ribonuclease PH
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAntczak, A.J. / Berger, J.M. / Lekin, T. / Segelke, B.W. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB) / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: 2.1 A Crystal structure of RNase PH from Mycobacterium tuberculosis.
Authors: Antczak, A.J. / Lekin, T. / Segelke, B.W. / Berger, J.M.
History
DepositionOct 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease PH
B: Ribonuclease PH
C: Ribonuclease PH
D: Ribonuclease PH
E: Ribonuclease PH
F: Ribonuclease PH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,73716
Polymers165,7886
Non-polymers95010
Water19,9431107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.529, 152.406, 83.512
Angle α, β, γ (deg.)90.00, 109.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribonuclease PH / RNase PH / tRNA nucleotidyltransferase


Mass: 27631.283 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: rph, rphA, Rv1340, MT1381, MTCY130.25, MTCY02B10.04 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold
References: UniProt: Q10628, UniProt: P9WGZ7*PLUS, tRNA nucleotidyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1107 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 298 K / pH: 7.5
Details: 22.5% PEG 2000, 0.1M MOPS pH 7.5, 0.085M NaH2PO4, 0.085M K2HPO4, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 2, 2005
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.09→78.811 Å / Num. obs: 399198 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.054 / Net I/σ(I): 22.2
Reflection shellResolution: 2.09→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.58 / Rsym value: 0.54 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R6M

1r6m


Resolution: 2.1→39.69 Å / Isotropic thermal model: ANISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED IN PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4614 5.01 %RANDOM
Rwork0.194 ---
all-92126 --
obs-92126 91.4 %-
Displacement parametersBiso mean: 39.67 Å2
Baniso -1Baniso -2Baniso -3
1-9.8368 Å2-0 Å2-7.3702 Å2
2---6.1408 Å2-0 Å2
3----3.6961 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10649 0 50 1107 11806
LS refinement shellResolution: 2.1→2.12 Å
RfactorNum. reflection% reflection
Rfree0.345 139 -
Rwork0.309 --
obs--80.19 %

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