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- PDB-3t0p: Crystal structure of a Putative DNA polymerase III beta subunit (... -

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Basic information

Entry
Database: PDB / ID: 3t0p
TitleCrystal structure of a Putative DNA polymerase III beta subunit (EUBREC_0002; ERE_29750) from Eubacterium rectale ATCC 33656 at 2.26 A resolution
ComponentsDNA polymerase III, beta subunit
KeywordsTRANSFERASE / DNA clamp / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
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, 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 / DNA polymerase III, beta sliding clamp / DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / 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 sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit / DNA polymerase III, beta sliding clamp / DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / : / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / R-1,2-PROPANEDIOL / Beta sliding clamp
Similarity search - Component
Biological speciesEubacterium rectale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.26 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative DNA polymerase III beta subunit (EUBREC_0002; ERE_29750) from Eubacterium rectale ATCC 33656 at 2.26 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.2Feb 1, 2023Group: 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III, beta subunit
B: DNA polymerase III, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,77829
Polymers85,1422
Non-polymers1,63627
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint14 kcal/mol
Surface area33440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.760, 95.560, 84.010
Angle α, β, γ (deg.)90.000, 115.940, 90.000
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING ANALYSIS AND SIZE-EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS THE STABLE OLIGOMERIC FORM IN SOLUTION.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase III, beta subunit


Mass: 42571.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale (bacteria) / Strain: ATCC 33656 / VPI 0990 / Gene: EUBREC_0002 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: C4Z938

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Non-polymers , 5 types, 272 molecules

#2: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 36.00% 1,2-propanediol, 0.100M calcium acetate, 0.1M sodium acetate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 9, 2011
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979361
ReflectionResolution: 2.26→29.632 Å / Num. obs: 41878 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 48.182 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.62
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.26-2.340.5781.8168168062195.6
2.34-2.430.4682.3160207679196.2
2.43-2.540.3773169608121196.4
2.54-2.680.2764.1175368403195.9
2.68-2.850.2015.6170338165196.1
2.85-3.070.128.5166958023195.7
3.07-3.370.06613.1158267658193.7
3.37-3.860.03619.6154497561189.6
3.86-4.850.02328.7151077446189.4
4.85-29.6320.0232.4153557660189.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.8.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.26→29.632 Å / Cor.coef. Fo:Fc: 0.9528 / Cor.coef. Fo:Fc free: 0.9316 / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. 1,2 ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT AND ACETATE (ACT), R-1,2-PROPANEDIOL (PGR) AND CHLORIDE ION (CL) FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 2098 5.03 %RANDOM
Rwork0.1733 ---
obs0.1752 41717 --
Displacement parametersBiso max: 190.21 Å2 / Biso mean: 57.389 Å2 / Biso min: 25.67 Å2
Baniso -1Baniso -2Baniso -3
1--2.8526 Å20 Å28.4313 Å2
2---1.8611 Å20 Å2
3---4.7136 Å2
Refinement stepCycle: LAST / Resolution: 2.26→29.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5716 0 104 245 6065
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2928SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes166HARMONIC2
X-RAY DIFFRACTIONt_gen_planes854HARMONIC5
X-RAY DIFFRACTIONt_it6001HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion856SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6967SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6009HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8087HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion3.03
LS refinement shellResolution: 2.26→2.32 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2718 155 5.18 %
Rwork0.218 2836 -
all0.2207 2991 -
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)
10.3307-0.15480.35631.0846-0.12671.0862-0.0499-0.08590.01570.26020.03640.0066-0.20950.04320.0135-0.0043-0.00080.0049-0.08790.0463-0.11466.026576.152659.058
20.4773-0.39490.44651.5063-0.27261.03290.14950.0753-0.0973-0.2388-0.06410.22950.1203-0.0557-0.0854-0.06160.0164-0.0779-0.0836-0.0036-0.0862-5.133456.665725.4111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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