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- PDB-1f21: DIVALENT METAL COFACTOR BINDING IN THE KINETIC FOLDING TRAJECTORY... -

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Basic information

Entry
Database: PDB / ID: 1f21
TitleDIVALENT METAL COFACTOR BINDING IN THE KINETIC FOLDING TRAJECTORY OF E. COLI RIBONUCLEASE HI
ComponentsRIBONUCLEASE HI
KeywordsHYDROLASE / RNase H / nuclease / RNase H* / ribnuclease H / metal-binding protein / protein folding
Function / homology
Function and homology information


DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / endonuclease activity / nucleic acid binding / magnesium ion binding / cytoplasm
Similarity search - Function
Ribonuclease HI / : / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsGoedken, E.R. / Keck, J.L. / Berger, J.M. / Marqusee, S.
CitationJournal: Protein Sci. / Year: 2000
Title: Divalent metal cofactor binding in the kinetic folding trajectory of Escherichia coli ribonuclease HI.
Authors: Goedken, E.R. / Keck, J.L. / Berger, J.M. / Marqusee, S.
History
DepositionMay 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 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: RIBONUCLEASE HI


Theoretical massNumber of molelcules
Total (without water)17,5271
Polymers17,5271
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.270, 40.830, 85.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RIBONUCLEASE HI


Mass: 17526.805 Da / Num. of mol.: 1 / Mutation: C13A, C63A, C133A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PSM101 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Y4, ribonuclease H
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.85 Å3/Da / Density % sol: 33.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes, pH 7.5, PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
PH range low: 8 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14-10 mg/mlprotein1drop
220 mMHEPES1reservoir
35-15 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 26582 / Num. obs: 24663 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.1 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.7
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4 % / Rmerge(I) obs: 0.136 / Num. unique all: 2603 / % possible all: 59.5
Reflection
*PLUS
Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 59.8 % / Mean I/σ(I) obs: 9.8

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.4→20 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2466 -Random
Rwork0.217 ---
all0.217 26582 --
obs-24663 92.8 %-
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 0 167 1378
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8

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