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- PDB-4s3i: Crystal structure of beta clamp from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 4s3i
TitleCrystal structure of beta clamp from Helicobacter pylori
ComponentsDNA polymerase III subunit betaDNA polymerase III holoenzyme
KeywordsTRANSFERASE / sliding DNA clamp / processivity promoting factor / DNA replication / DNA
Function / homology
Function and homology information


DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function
DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit ...DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / : / Roll / Alpha Beta
Similarity search - Domain/homology
: / Beta sliding clamp
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.946 Å
AuthorsPandey, P. / Tarique, K.F. / Abdul Rehman, S.A. / Gourinath, S.
CitationJournal: Sci Rep / Year: 2016
Title: Structural insight into beta-Clamp and its interaction with DNA Ligase in Helicobacter pylori.
Authors: Pandey, P. / Tarique, K.F. / Mazumder, M. / Rehman, S.A. / Kumari, N. / Gourinath, S.
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.3Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase III subunit beta
B: DNA polymerase III subunit beta


Theoretical massNumber of molelcules
Total (without water)87,0242
Polymers87,0242
Non-polymers00
Water7,044391
1
A: DNA polymerase III subunit beta

A: DNA polymerase III subunit beta


Theoretical massNumber of molelcules
Total (without water)87,0242
Polymers87,0242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2400 Å2
ΔGint-9 kcal/mol
Surface area35370 Å2
MethodPISA
2
B: DNA polymerase III subunit beta

B: DNA polymerase III subunit beta


Theoretical massNumber of molelcules
Total (without water)87,0242
Polymers87,0242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_856-x+3,y,-z+11
Buried area2370 Å2
ΔGint-9 kcal/mol
Surface area35210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.502, 65.474, 88.900
Angle α, β, γ (deg.)90.00, 116.03, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 375
2010B2 - 375

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Components

#1: Protein DNA polymerase III subunit beta / DNA polymerase III holoenzyme / beta clamp


Mass: 43511.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: C694_02570 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: K4NBW6, UniProt: O25242*PLUS, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 6% PEG20000, 20% PEG550 MME, 0.1 M HEPES+MOPS, pH 7.3, 0.2 M ammonium citrate dibasic, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 4, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.946→79.886 Å / Num. all: 62706 / Num. obs: 60925 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Rsym value: 0.062 / Net I/σ(I): 38.35
Reflection shellResolution: 1.946→1.98 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 2.88 / Rsym value: 0.49 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0085refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RKI

4rki


Resolution: 1.946→30.082 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU ML: 0.22 / σ(F): 1.36 / Phase error: 45.85 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2504 3073 5.07 %
Rwork0.2142 --
obs0.2161 60560 96.52 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.528 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.0742 Å20 Å2-1.223 Å2
2--6.0045 Å20 Å2
3---1.0697 Å2
Refine analyzeLuzzati coordinate error obs: 0.397 Å
Refinement stepCycle: LAST / Resolution: 1.946→30.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5934 0 0 391 6325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086048
X-RAY DIFFRACTIONf_angle_d1.1148144
X-RAY DIFFRACTIONf_dihedral_angle_d15.4192296
X-RAY DIFFRACTIONf_chiral_restr0.075950
X-RAY DIFFRACTIONf_plane_restr0.0041028
Refine LS restraints NCS

Ens-ID: 1 / Number: 49242 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9456-1.9760.3363440.35031114X-RAY DIFFRACTION41
1.976-2.00830.32051510.3152588X-RAY DIFFRACTION97
2.0083-2.0430.34031470.29182690X-RAY DIFFRACTION100
2.043-2.08010.32351330.29042679X-RAY DIFFRACTION100
2.0801-2.12010.331530.27842696X-RAY DIFFRACTION100
2.1201-2.16340.26821310.27372692X-RAY DIFFRACTION100
2.1634-2.21040.30341340.26252649X-RAY DIFFRACTION100
2.2104-2.26180.28071420.24252707X-RAY DIFFRACTION100
2.2618-2.31830.30291460.23362656X-RAY DIFFRACTION100
2.3183-2.3810.29031640.2292694X-RAY DIFFRACTION100
2.381-2.4510.30121490.23822697X-RAY DIFFRACTION100
2.451-2.53010.2621480.23452680X-RAY DIFFRACTION100
2.5301-2.62050.27721380.24162713X-RAY DIFFRACTION100
2.6205-2.72530.2641380.23522679X-RAY DIFFRACTION100
2.7253-2.84930.31271210.23172747X-RAY DIFFRACTION100
2.8493-2.99940.27031380.22422677X-RAY DIFFRACTION100
2.9994-3.18710.27441450.21842719X-RAY DIFFRACTION100
3.1871-3.43290.23941530.20332697X-RAY DIFFRACTION100
3.4329-3.77770.20361450.19352703X-RAY DIFFRACTION100
3.7777-4.3230.20321480.16482727X-RAY DIFFRACTION100
4.323-5.44120.19621500.15932709X-RAY DIFFRACTION99
5.4412-30.08550.22831550.19582574X-RAY DIFFRACTION92
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)
10.64980.0375-0.48120.029-0.25761.7599-0.0662-0.01560.16490.0067-0.0226-0.0598-0.03030.2150.07510.2978-0.039-0.00370.2460.04980.464558.839665.534411.2075
20.6254-0.135-0.23060.02950.0910.33030.10130.26210.0154-0.038-0.12610.0337-0.0355-0.174-0.02260.1377-0.010.01680.164-0.11440.232686.655732.798928.737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:374)
2X-RAY DIFFRACTION2(chain B and resseq 1:374)

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