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- PDB-4z0u: RNase HI/SSB-Ct complex -

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Basic information

Entry
Database: PDB / ID: 4z0u
TitleRNase HI/SSB-Ct complex
Components
  • Ribonuclease H
  • SSB-Ct Peptide
KeywordsHydrolase/Peptide / Ribonuclease / peptide complex / Hydrolase-Peptide complex
Function / homology
Function and homology information


single-stranded DNA-binding protein complex / DNA replication, removal of RNA primer / SOS response / nucleoid / replisome / recombinational repair / ribonuclease H / mismatch repair / enzyme activator activity / DNA-templated DNA replication ...single-stranded DNA-binding protein complex / DNA replication, removal of RNA primer / SOS response / nucleoid / replisome / recombinational repair / ribonuclease H / mismatch repair / enzyme activator activity / DNA-templated DNA replication / RNA-DNA hybrid ribonuclease activity / single-stranded DNA binding / nucleic acid binding / DNA replication / magnesium ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Ribonuclease HI / Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / : / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain ...Ribonuclease HI / Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / : / 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 / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonuclease H / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesEscherichia coli O139:H28 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPetzold, C. / Keck, J.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM0987885 United States
National Science Foundation (NSF, United States)DGE-1256259 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity.
Authors: Petzold, C. / Marceau, A.H. / Miller, K.H. / Marqusee, S. / Keck, J.L.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease H
B: Ribonuclease H
D: SSB-Ct Peptide
E: SSB-Ct Peptide


Theoretical massNumber of molelcules
Total (without water)37,8474
Polymers37,8474
Non-polymers00
Water1,49583
1
A: Ribonuclease H
D: SSB-Ct Peptide


Theoretical massNumber of molelcules
Total (without water)18,9232
Polymers18,9232
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-4 kcal/mol
Surface area8690 Å2
MethodPISA
2
B: Ribonuclease H
E: SSB-Ct Peptide


Theoretical massNumber of molelcules
Total (without water)18,9232
Polymers18,9232
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-4 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.498, 64.855, 79.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Ribonuclease H / RNase H


Mass: 17622.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O139:H28 (bacteria) / Strain: E24377A / ETEC / Gene: rnhA, EcE24377A_0219 / Production host: Escherichia coli (E. coli) / References: UniProt: A7ZHV1, ribonuclease H
#2: Protein/peptide SSB-Ct Peptide


Mass: 1300.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P0AGE0*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: sodium citrate, HEPES, glycerol, 1,4 dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 21970 / % possible obs: 99.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.033 / Rrim(I) all: 0.068 / Χ2: 1.34 / Net I/av σ(I): 27.436 / Net I/σ(I): 11.5 / Num. measured all: 88106
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.90.57510860.8360.3340.6670.92699.6
2.03-2.0740.49610750.870.2850.5740.99299.9
2.07-2.1140.44710890.880.2540.5151.062100
2.11-2.154.10.34610670.9330.1960.3990.942100
2.15-2.24.10.31310680.9350.1780.3611.021100
2.2-2.254.10.26310970.9490.150.3031.06100
2.25-2.314.10.24410780.9550.1390.2811.084100
2.31-2.374.10.21710820.9620.1240.251.088100
2.37-2.444.10.1810920.9690.1020.2081.157100
2.44-2.524.10.1610840.9750.0910.1841.236100
2.52-2.614.10.13910940.9820.0780.161.517100
2.61-2.714.10.11610900.9850.0650.1331.558100
2.71-2.844.10.10110860.990.0570.1171.47899.9
2.84-2.994.10.07111000.9960.040.0811.357100
2.99-3.174.10.05410950.9960.030.0631.343100
3.17-3.4240.05211150.9970.0290.061.956100
3.42-3.763.90.04810980.9960.0270.0552.449100
3.76-4.3140.03311270.9980.0180.0381.768100
4.31-5.433.90.02711420.9990.0160.0321.4499.9
5.43-503.60.02512050.9990.0150.0291.37798.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.62 Å38.68 Å
Translation6.62 Å38.68 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.44 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24089 1095 5 %RANDOM
Rwork0.2111 ---
obs0.21262 20856 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.569 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å20 Å2
2--1.32 Å2-0 Å2
3----2.77 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 0 83 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192694
X-RAY DIFFRACTIONr_bond_other_d0.0010.022548
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.9313662
X-RAY DIFFRACTIONr_angle_other_deg0.69635871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4715342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35823.971136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37415477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4751521
X-RAY DIFFRACTIONr_chiral_restr0.0640.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02652
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8873.981296
X-RAY DIFFRACTIONr_mcbond_other1.8873.9791295
X-RAY DIFFRACTIONr_mcangle_it3.075.9531620
X-RAY DIFFRACTIONr_mcangle_other3.0695.9541621
X-RAY DIFFRACTIONr_scbond_it2.1124.4211398
X-RAY DIFFRACTIONr_scbond_other2.1124.4211398
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5416.4812028
X-RAY DIFFRACTIONr_long_range_B_refined6.42332.3413079
X-RAY DIFFRACTIONr_long_range_B_other6.21832.2713062
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 61 -
Rwork0.301 1504 -
obs--96.9 %

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