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- PDB-2gno: Crystal structure of a dna polymerase iii, gamma subunit-related ... -

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Basic information

Entry
Database: PDB / ID: 2gno
TitleCrystal structure of a dna polymerase iii, gamma subunit-related protein (tm0771) from thermotoga maritima msb8 at 2.00 A resolution
ComponentsDNA polymerase III, gamma subunit-related protein
KeywordsREPLICATION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


DNA-templated DNA replication / DNA binding
Similarity search - Function
DNA polymerase III clamp loader domain like / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle ...DNA polymerase III clamp loader domain like / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-ETHOXYETHANOL / Unknown ligand / DNA polymerase III, gamma subunit-related protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of DNA polymerase III, gamma subunit-related protein (tm0771) from Thermotoga maritima at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 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
Remark 999SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 9-312 OF THE TM0771 SEQUENCE. A SMALL AMOUNT OF PROTEIN WITH THE TAG UNCLEAVED REMAINED IN THE SAMPLE AFTER PURIFICATION. A SERIES OF DIFFERENT LENGTH N-TERMINAL TRUNCATIONS WERE TRIED TO IMPROVE DIFFRACTION QUALITY FROM THIS TARGET. THE CONSTRUCT WITH RESIDUES 1-8 ELIMINATED PRODUCED THE BEST DIFFRACTING CRYSTAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III, gamma subunit-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6895
Polymers35,4861
Non-polymers2034
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.560, 135.560, 35.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein DNA polymerase III, gamma subunit-related protein


Mass: 35485.527 Da / Num. of mol.: 1 / Fragment: residues 9-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0771 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZM9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.31 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.2
Details: 35.0% 2-ethoxyethanol, 0.2M NaCl, 0.1M Na,K-Phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979224, 0.918370, 0.978940
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2005 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9792241
20.918371
30.978941
ReflectionResolution: 2→27.9 Å / Num. obs: 22105 / % possible obs: 94.7 % / Biso Wilson estimate: 42.314 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 11.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.070.41526860358083.8
2.07-2.150.3142.77034371190.1
2.15-2.250.2513.37757406092.2
2.25-2.370.1844.57788407293.6
2.37-2.520.1256.37968416697
2.52-2.710.0938.37792408897.8
2.71-2.990.06710.98351435398.7
2.99-3.420.04615.58021423199.7
3.420.02525.17896419999.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SHARPV. 1phasing
RefinementMethod to determine structure: MAD / Resolution: 2→27.94 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.889 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.197
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). 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. 3). TWO MOLECULES OF 2-ETHOXYETHANOL FROM THE CRYSTALLIZATION BUFFER HAS BEEN MODELED INTO THE STRUCTURE. 4). AN UNKNOWN LIGAND HAS BEEN MODELED INTO THE STRUCTURE BETWEEN THE SIDECHAINS OF LEU 168 AND ARG 254. 5.) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1130 5.1 %RANDOM
Rwork0.22 ---
obs0.223 22103 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.573 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2---0.96 Å20 Å2
3---1.91 Å2
Refinement stepCycle: LAST / Resolution: 2→27.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 17 107 2470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222466
X-RAY DIFFRACTIONr_bond_other_d0.0030.022343
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9893341
X-RAY DIFFRACTIONr_angle_other_deg1.18835432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0995309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.18224.112107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.31915458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2521518
X-RAY DIFFRACTIONr_chiral_restr0.1070.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022707
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02487
X-RAY DIFFRACTIONr_nbd_refined0.180.3532
X-RAY DIFFRACTIONr_nbd_other0.1230.32275
X-RAY DIFFRACTIONr_nbtor_refined0.1650.51206
X-RAY DIFFRACTIONr_nbtor_other0.0810.51307
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.5174
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1090.355
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.517
X-RAY DIFFRACTIONr_mcbond_it1.42731513
X-RAY DIFFRACTIONr_mcbond_other0.3853605
X-RAY DIFFRACTIONr_mcangle_it2.4252458
X-RAY DIFFRACTIONr_scbond_it4.2088977
X-RAY DIFFRACTIONr_scangle_it6.1411881
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 95 -
Rwork0.257 1504 -
obs-1599 99.13 %
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)
12.27393.3447-0.04586.0604-2.5086.0805-0.47660.82180.132-0.8650.6166-0.14550.0443-1.0041-0.1401-0.021-0.0383-0.02240.19350.0757-0.094719.29678.545227.1236
22.99191.5443-2.41874.5978-2.29674.9265-0.093-0.08270.09720.15650.03080.13390.2259-0.33910.06220.0123-0.02680.00390.0088-0.0152-0.035322.37572.964939.6628
33.7286-1.51470.0921.66630.26960.74210.29610.17970.1402-0.444-0.2409-0.11790.3113-0.1436-0.05520.2185-0.01960.1473-0.0902-0.0095-0.086736.565863.071326.8708
42.42660.6897-0.41043.91580.1591.81750.1276-0.04520.03430.02630.08680.1446-0.0776-0.0887-0.21440.01630.02810.0464-0.0564-0.0088-0.009744.116944.932736.3526
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
1111 - 294 - 22
2230 - 12523 - 118
33126 - 197119 - 190
44198 - 306191 - 299

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