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- PDB-5vaz: Crystal structure of a DNA primase domain from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5vaz
TitleCrystal structure of a DNA primase domain from Pseudomonas aeruginosa
ComponentsDNA primasePrimase
KeywordsTRANSFERASE / structural genomics / DNA-binding / primase / truncation / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


primosome complex / DNA primase activity / DNA replication, synthesis of primer / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
DnaG, RNA polymerase domain, helical bundle / DNA primase, catalytic core, N-terminal domain / DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / DNA primase DNAg catalytic core, N-terminal domain / Pheromone ER-1 / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Toprim domain ...DnaG, RNA polymerase domain, helical bundle / DNA primase, catalytic core, N-terminal domain / DNA primase DnaG, DnaB-binding domain / DNA primase DnaG DnaB-binding / DNA primase DnaG DnaB-binding / DNA primase DNAg catalytic core, N-terminal domain / Pheromone ER-1 / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Toprim domain / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain / DNA Primase, CHC2-type zinc finger / DNA primase, catalytic core, N-terminal domain superfamily / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / TOPRIM / Toprim domain profile. / TOPRIM domain / Alpha-Beta Complex / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a DNA primase domain from Pseudomonas aeruginosa
Authors: Edwards, T.E. / Conrady, D.G. / Lorimer, D. / Manoil, C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMar 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
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: DNA primase
B: DNA primase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,77017
Polymers86,3292
Non-polymers1,44115
Water3,639202
1
A: DNA primase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7417
Polymers43,1651
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA primase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,02910
Polymers43,1651
Non-polymers8659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-200 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.300, 142.300, 106.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-679-

HOH

21B-607-

HOH

31B-710-

HOH

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Components

#1: Protein DNA primase / Primase


Mass: 43164.703 Da / Num. of mol.: 2 / Fragment: unp residues 106-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: dnaG, PA0577 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I5W0, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 3.6 Å3/Da / Density % sol: 65.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PsaeA.00153.a.B7.PS38108 at 18.8 mg/mL against Top96 screen condition A4: 0.1 M Tris pH 8.5, 2 M ammonium sulfate, cryo-protected with 20% EG, crystal tracking ID 28610a4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→48.866 Å / Num. obs: 48947 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.486 % / Biso Wilson estimate: 47.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.065 / Χ2: 1.043 / Net I/σ(I): 21.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.467.60.5343.6836070.9010.573100
2.46-2.537.6210.4374.5234780.9380.469100
2.53-2.67.5870.3635.4333900.9570.39100
2.6-2.687.6060.2866.8733180.9710.307100
2.68-2.777.5940.2358.4231870.980.252100
2.77-2.877.5840.18210.6131000.9890.196100
2.87-2.987.5840.14513.2830030.9920.155100
2.98-3.17.5890.11816.0328690.9940.126100
3.1-3.247.5170.0920.2328030.9960.097100
3.24-3.397.5090.07324.8926240.9970.078100
3.39-3.587.4570.0629.5925370.9980.064100
3.58-3.797.4050.0534.8523930.9980.054100
3.79-4.067.3870.04538.0322480.9990.048100
4.06-4.387.3430.04140.9220900.9990.044100
4.38-4.87.330.03743.2919610.9990.04100
4.8-5.377.3630.03643.9617720.9990.038100
5.37-6.27.3490.03741.9915630.9990.04100
6.2-7.597.2760.03443.9813420.9990.036100
7.59-10.737.0340.02948.0510600.9990.03199.9
10.73-48.8666.2810.02845.966020.9990.03197.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dd9

1dd9


Resolution: 2.4→48.866 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.1
RfactorNum. reflection% reflection
Rfree0.214 2109 4.31 %
Rwork0.1867 --
obs0.1879 48914 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.32 Å2 / Biso mean: 59.8904 Å2 / Biso min: 25.69 Å2
Refinement stepCycle: final / Resolution: 2.4→48.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4848 0 75 202 5125
Biso mean--119.05 56.39 -
Num. residues----641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075031
X-RAY DIFFRACTIONf_angle_d0.8836836
X-RAY DIFFRACTIONf_chiral_restr0.049741
X-RAY DIFFRACTIONf_plane_restr0.007906
X-RAY DIFFRACTIONf_dihedral_angle_d13.9392991
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.45580.28471330.245930833216
2.4558-2.51720.31761540.232130713225
2.5172-2.58520.30851210.23131303251
2.5852-2.66130.25821460.213230623208
2.6613-2.74720.2551460.212830803226
2.7472-2.84540.24611260.208431223248
2.8454-2.95930.23931610.218930923253
2.9593-3.0940.27731290.22730963225
3.094-3.2570.25431490.21430923241
3.257-3.46110.23671460.207431253271
3.4611-3.72820.22251520.186431153267
3.7282-4.10320.20211540.164931043258
4.1032-4.69650.15961310.144631503281
4.6965-5.91550.16781380.166331963334
5.9155-48.87640.17811230.176632873410
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)
13.16271.03920.85277.48732.50862.78-0.1727-0.03090.19830.0037-0.29931.4156-0.1119-0.41940.45280.4668-0.0159-0.09310.4087-0.10480.655436.0878-24.8378-7.6228
22.69690.2901-2.43061.86872.47916.5025-0.03320.0384-0.0078-0.3352-0.08670.4192-0.3044-0.62160.06830.52540.0179-0.15010.31730.03410.499546.6311-8.8979-2.3974
32.9857-0.17020.91280.8924-0.27451.07940.0005-0.1195-0.3071-0.16870.06960.07920.2514-0.1653-0.05350.5222-0.01570.00880.1873-0.01130.3661.019-10.38066.5183
42.7828-0.63711.73482.7192-1.88424.0951-0.17170.3487-0.344-0.2221-0.1955-0.6369-0.13580.93080.26330.49920.01170.06310.28980.04780.454879.2923-6.72183.9318
50.98980.3843-0.64881.3337-0.09810.4358-0.89480.7994-0.3629-1.37060.5711-0.39140.8409-0.25680.09761.6999-0.6220.30620.5426-0.02920.58981.767116.4455-38.5834
64.53695.1288-2.10455.7803-2.09641.4625-0.76410.47580.1007-0.9860.6007-0.01280.5702-0.24850.10580.7083-0.18260.00190.3841-0.02440.350381.413222.9007-29.8014
72.63370.95410.70581.27651.76816.7741-0.10920.12580.2046-0.03530.3123-0.0754-0.04760.1858-0.20140.5447-0.05880.01780.22170.0230.350870.726914.5028-14.709
80.48430.4735-0.15410.59920.01532.4081-0.21990.0998-0.0742-0.08590.1872-0.10130.45910.05930.03580.5811-0.03220.01320.2165-0.03730.357769.77495.3755-6.7501
96.1553-3.62751.84872.5505-1.6941.577-0.5022-0.21130.18410.42920.27160.1039-0.5089-0.13780.17160.59020.0078-0.00430.2026-0.01260.384460.381314.20947.1057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 114 through 250 )A114 - 250
2X-RAY DIFFRACTION2chain 'A' and (resid 251 through 293 )A251 - 293
3X-RAY DIFFRACTION3chain 'A' and (resid 294 through 405 )A294 - 405
4X-RAY DIFFRACTION4chain 'A' and (resid 406 through 432 )A406 - 432
5X-RAY DIFFRACTION5chain 'B' and (resid 116 through 160 )B116 - 160
6X-RAY DIFFRACTION6chain 'B' and (resid 161 through 278 )B161 - 278
7X-RAY DIFFRACTION7chain 'B' and (resid 279 through 331 )B279 - 331
8X-RAY DIFFRACTION8chain 'B' and (resid 332 through 405 )B332 - 405
9X-RAY DIFFRACTION9chain 'B' and (resid 406 through 436 )B406 - 436

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