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- PDB-8ipw: The sturecture of Legionella effector protein MavL with ADPR -

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Basic information

Entry
Database: PDB / ID: 8ipw
TitleThe sturecture of Legionella effector protein MavL with ADPR
ComponentsMavL
KeywordsPROTEIN BINDING / MavL / ADPR
Function / homologyChem-AR6 / :
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsOuyang, S. / Hongxin, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82172287 China
CitationJournal: To Be Published
Title: The sturecture of Legionella effector protein MavL with ADPR
Authors: Ouyang, S. / Hongxin, G.
History
DepositionMar 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MavL
B: MavL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9074
Polymers80,7892
Non-polymers1,1192
Water27015
1
A: MavL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9542
Polymers40,3941
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MavL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9542
Polymers40,3941
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.790, 108.320, 129.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MavL


Mass: 40394.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_12725 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F2R2
#2: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 289.15 K / Method: counter-diffusion
Details: 0.25 M potassium citrate tribasic monohydrate,18%PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→29.11 Å / Num. obs: 30117 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.998 / Net I/σ(I): 11.8
Reflection shellResolution: 2.38→2.44 Å / Num. unique obs: 1970 / CC1/2: 0.609

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (24-FEB-2021)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OMI

6omi


Resolution: 2.35→25.24 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.432 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.419 / SU Rfree Blow DPI: 0.257 / SU Rfree Cruickshank DPI: 0.263
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 1998 6.63 %RANDOM
Rwork0.2095 ---
obs0.2126 30117 98.4 %-
Displacement parametersBiso mean: 74.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.9453 Å20 Å20 Å2
2--18.0131 Å20 Å2
3----16.0679 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.35→25.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5588 0 72 16 5676
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095802HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.037890HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1945SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes972HARMONIC5
X-RAY DIFFRACTIONt_it5802HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion20.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion751SEMIHARMONIC5
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_contact4338SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.37 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3033 -6.63 %
Rwork0.3172 563 -
all0.3162 603 -
obs--99.01 %
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)
13.5054-1.2747-0.18322.20060.45030.510.07590.25560.3263-0.0833-0.0621-0.3829-0.07370.1047-0.0138-0.093-0.03420.1058-0.10070.06110.1553-19.2433-0.3188-6.796
22.155-0.89930.19382.52480.3641.1777-0.1163-0.34230.41650.3748-0.0143-0.38730.01630.16830.1306-0.0522-0.0506-0.0074-0.1147-0.09290.2104-22.54167.684510.9255
31.4198-0.0849-0.60421.12031.37261.76230.0520.12560.374-0.0137-0.1417-0.0345-0.078-0.04180.08970.0063-0.01080.0733-0.15570.02530.2975-33.72378.73920.0874
41.6682-0.4802-0.10512.04520.92351.46590.00270.63690.3486-0.3153-0.13350.0082-0.1415-0.03010.1309-0.0457-0.00510.0853-0.13820.16070.1383-30.57015.1773-12.8835
52.062.3537-0.4017.7532-0.52680.27720.1262-0.1983-0.0734-0.0966-0.0395-0.08560.1429-0.0402-0.08670.0931-0.018-0.04720.00130.0418-0.2065-27.738814.7217-42.9833
61.79650.4596-0.30933.0359-0.93881.09560.3593-0.4330.22150.4304-0.2639-0.1391-0.1517-0.0915-0.09530.0609-0.1488-0.00640.0812-0.1123-0.2003-26.510628.4393-31.8687
72.39721.30750.38124.0704-0.71452.07740.15290.16690.0458-0.874-0.4096-0.78330.48150.40230.25670.09210.13610.149-0.07370.0069-0.1184-18.516223.958-52.0937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|42 - A|161 }
2X-RAY DIFFRACTION2{ A|162 - A|282 }
3X-RAY DIFFRACTION3{ A|283 - A|347 }
4X-RAY DIFFRACTION4{ A|348 - A|404 }
5X-RAY DIFFRACTION5{ B|42 - B|161 }
6X-RAY DIFFRACTION6{ B|162 - B|347 }
7X-RAY DIFFRACTION7{ B|348 - B|402 }

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