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- PDB-7p0h: Crystal structure of Helicobacter pylori ComF fused to an artific... -

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Basic information

Entry
Database: PDB / ID: 7p0h
TitleCrystal structure of Helicobacter pylori ComF fused to an artificial alphaREP crystallization helper(named B2)
ComponentsHelicobacter pylori ComF fused to an artificial alphaREP crystallization helper (named B2)
KeywordsRECOMBINATION / Competence protein
Function / homologyPhosphoribosyltransferase-like / Phosphoribosyltransferase domain / metal ion binding / Chem-PRP / Amidophosphoribosyltransferase
Function and homology information
Biological speciesSynthetic construct (others)
Helicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.499 Å
AuthorsCelma, L. / Walbott, H. / Legrand, P. / Quevillon-Cheruel, S.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
CitationJournal: Nat Commun / Year: 2022
Title: ComFC mediates transport and handling of single-stranded DNA during natural transformation.
Authors: Damke, P.P. / Celma, L. / Kondekar, S.M. / Di Guilmi, A.M. / Marsin, S. / Depagne, J. / Veaute, X. / Legrand, P. / Walbott, H. / Vercruyssen, J. / Guerois, R. / Quevillon-Cheruel, S. / Radicella, J.P.
History
DepositionJun 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 9, 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: Helicobacter pylori ComF fused to an artificial alphaREP crystallization helper (named B2)
B: Helicobacter pylori ComF fused to an artificial alphaREP crystallization helper (named B2)
C: Helicobacter pylori ComF fused to an artificial alphaREP crystallization helper (named B2)
D: Helicobacter pylori ComF fused to an artificial alphaREP crystallization helper (named B2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,79234
Polymers188,4874
Non-polymers3,30630
Water5,080282
1
A: Helicobacter pylori ComF fused to an artificial alphaREP crystallization helper (named B2)
C: Helicobacter pylori ComF fused to an artificial alphaREP crystallization helper (named B2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,17220
Polymers94,2432
Non-polymers1,92918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-95 kcal/mol
Surface area35350 Å2
MethodPISA
2
B: Helicobacter pylori ComF fused to an artificial alphaREP crystallization helper (named B2)
D: Helicobacter pylori ComF fused to an artificial alphaREP crystallization helper (named B2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,62014
Polymers94,2432
Non-polymers1,37712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8890 Å2
ΔGint-96 kcal/mol
Surface area35300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.880, 87.980, 122.790
Angle α, β, γ (deg.)80.230, 76.440, 76.390
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Helicobacter pylori ComF fused to an artificial alphaREP crystallization helper (named B2)


Mass: 47121.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic construct (others), (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: HP_1473
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O26008
#3: Sugar
ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H13O14P3 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 308 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2M Tri-potassium citrate PEG 3350 18% (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 10, 2017 / Details: KB Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.49→46.47 Å / Num. obs: 77488 / % possible obs: 98.4 % / Redundancy: 11.6 % / Biso Wilson estimate: 79.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.029 / Rrim(I) all: 0.099 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.49-2.5610.72.8455784153980.4830.8812.9860.692.6
11.15-46.4110.60.04891338650.9980.0160.05171.398.3

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Processing

Software
NameVersionClassification
STARANISO1.10.9 (13-Dec-2017)data scaling
BUSTER2.10.3 (20-MAY-2020)refinement
PDB_EXTRACT3.27data extraction
XDSNov 11, 2017data reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: SAD / Resolution: 2.499→46.47 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.661 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.574 / SU Rfree Blow DPI: 0.288 / SU Rfree Cruickshank DPI: 0.3 / Details: Dataset anisotropically truncated by STARANISO
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 3156 5 %RANDOM
Rwork0.2209 ---
obs0.2221 63118 80.2 %-
Displacement parametersBiso max: 146.65 Å2 / Biso mean: 69.74 Å2 / Biso min: 28.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.5785 Å2-0.2807 Å20.3187 Å2
2--1.5245 Å2-0.6682 Å2
3----2.1029 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: final / Resolution: 2.499→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12672 0 184 282 13138
Biso mean--79.81 54.88 -
Num. residues----1644
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4732SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2188HARMONIC5
X-RAY DIFFRACTIONt_it13014HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1700SEMIHARMONIC5
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_contact9664SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13014HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg17546HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion18.9
LS refinement shellResolution: 2.5→2.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2724 60 4.75 %
Rwork0.2559 1203 -
all0.2567 1263 -
obs--29.43 %
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)
12.72140.59890.7960.1002-0.02461.95720.2129-0.0899-0.2260.0835-0.08080.02190.0653-0.1213-0.1321-0.0720.0678-0.0894-0.0853-0.0255-0.0229-0.146448.38-25.8988
20.48230.2716-1.0390.3377-0.75892.67810.0392-0.22910.02880.08470.06470.0066-0.29190.1872-0.10390.10650.02310.101-0.0692-0.0524-0.026328.199788.6361-54.5223
33.0895-0.887-0.66360.5296-0.28711.6580.3427-0.03150.4071-0.1338-0.13930.02340.0999-0.0701-0.2034-0.1702-0.07830.1642-0.041-0.05140.00160.406897.12271.4032
40.9018-1.1712.14730.84920.17855.22610.05920.5055-0.23310.06860.1336-0.03110.58040.1274-0.19280.2104-0.1786-0.10730.0484-0.0479-0.118128.363256.459729.766
52.18150.6644-0.52220.49730.04141.4290.1298-0.0750.16610.1989-0.12310.00720.00230.1537-0.0067-0.17250.07090.0277-0.0007-0.0012-0.029434.408692.786-31.8459
60.65710.9891.13890.12391.44843.31390.0518-0.25570.03790.20930.09150.08590.4981-0.0729-0.14330.26410.0405-0.2187-0.08520.0567-0.06726.221446.6824-49.2522
72.9605-0.42941.49380.24990.45372.1370.40080.0529-0.22260.0291-0.2169-0.08210.16680.0222-0.1839-0.058-0.131-0.0913-0.04030.0793-0.088234.53652.81116.7586
81.337-1.4614-2.15891.08381.84723.87640.22190.49290.1929-0.3534-0.0235-0.1487-0.6435-0.2286-0.19840.1272-0.10090.14660.02140.0261-0.04526.575798.623624.7428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|16 - A|231 }A16 - 231
2X-RAY DIFFRACTION2{ A|232 - A|426 A|501 - A|503 }A232 - 426
3X-RAY DIFFRACTION2{ A|232 - A|426 A|501 - A|503 }A501 - 503
4X-RAY DIFFRACTION3{ B|16 - B|231 }B16 - 231
5X-RAY DIFFRACTION4{ B|232 - B|426 B|501 - B|503 }B232 - 426
6X-RAY DIFFRACTION4{ B|232 - B|426 B|501 - B|503 }B501 - 503
7X-RAY DIFFRACTION5{ C|16 - C|231 }C16 - 231
8X-RAY DIFFRACTION6{ C|232 - C|426 C|501 - C|503 }C232 - 426
9X-RAY DIFFRACTION6{ C|232 - C|426 C|501 - C|503 }C501 - 503
10X-RAY DIFFRACTION7{ D|16 - D|231 }D16 - 231
11X-RAY DIFFRACTION8{ D|232 - D|426 D|501 - D|503 }D232 - 426
12X-RAY DIFFRACTION8{ D|232 - D|426 D|501 - D|503 }D501 - 503

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