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- PDB-7qrl: LytM domain of DipM, a coordinator of a complex net of autolysins... -

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Basic information

Entry
Database: PDB / ID: 7qrl
TitleLytM domain of DipM, a coordinator of a complex net of autolysins in Caulobacter crescentus
Components(DipM) x 2
KeywordsCELL CYCLE / LytM factor Autolysin activator
Function / homology
Function and homology information


metalloendopeptidase activity
Similarity search - Function
Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. ...Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBatuecas, M.T. / Miguel-Ruano, V. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-90030-P Spain
CitationJournal: Nat Commun / Year: 2023
Title: LytM domain of DipM, a coordinator of a complex net of autolysins in Caulobacter crescentus
Authors: Batuecas, M.T. / Miguel-Ruano, V. / Hermoso, J.A.
History
DepositionJan 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DipM
B: DipM
C: DipM
D: DipM


Theoretical massNumber of molelcules
Total (without water)61,7504
Polymers61,7504
Non-polymers00
Water8,485471
1
A: DipM


Theoretical massNumber of molelcules
Total (without water)15,1231
Polymers15,1231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DipM


Theoretical massNumber of molelcules
Total (without water)15,1231
Polymers15,1231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DipM


Theoretical massNumber of molelcules
Total (without water)15,7521
Polymers15,7521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DipM


Theoretical massNumber of molelcules
Total (without water)15,7521
Polymers15,7521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.869, 105.839, 108.431
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAARGARGAA467 - 6091 - 143
21ALAALAARGARGBB467 - 6091 - 143
12ALAALAPROPROAA467 - 6081 - 142
22ALAALAPROPROCC467 - 6087 - 148
13ALAALAPROPROAA467 - 6081 - 142
23ALAALAPROPRODD467 - 6087 - 148
14ALAALAPROPROBB467 - 6081 - 142
24ALAALAPROPROCC467 - 6087 - 148
15ALAALAPROPROBB467 - 6081 - 142
25ALAALAPROPRODD467 - 6087 - 148
16THRTHRARGARGCC461 - 6091 - 149
26THRTHRARGARGDD461 - 6091 - 149

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein DipM / Peptidase / M23/M37 family


Mass: 15123.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Strain: ATCC 19089 / CB15 / Gene: dipM, CC_1996 / Plasmid: pTB146 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9A6T7
#2: Protein DipM / Peptidase / M23/M37 family


Mass: 15751.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Strain: ATCC 19089 / CB15 / Gene: dipM, CC_1996 / Plasmid: pTB146 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9A6T7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 0.02M Magnesium chloride, 0.1M Hepes pH 7.5 and 22% Polyacrylic acid sodium salt 5100 .
Temp details: 30% polyethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979185 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979185 Å / Relative weight: 1
ReflectionResolution: 2.25→49.75 Å / Num. obs: 36758 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 0.99 / Rpim(I) all: 0.102 / Net I/σ(I): 8
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3319 / CC1/2: 0.703 / Rpim(I) all: 0.474 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KVP

5kvp


Resolution: 2.25→49.75 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.728 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 1754 4.8 %RANDOM
Rwork0.1877 ---
obs0.1892 34958 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.39 Å2 / Biso mean: 25.599 Å2 / Biso min: 11.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0 Å20 Å2
2--1.54 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 2.25→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4352 0 0 471 4823
Biso mean---32.34 -
Num. residues----584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134530
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154378
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.656163
X-RAY DIFFRACTIONr_angle_other_deg1.3041.58310082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3065595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6522.264212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51115732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0151529
X-RAY DIFFRACTIONr_chiral_restr0.070.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021012
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A42650.07
12B42650.07
21A39870.11
22C39870.11
31A39700.12
32D39700.12
41B39890.12
42C39890.12
51B39820.12
52D39820.12
61C43260.07
62D43260.07
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 121 -
Rwork0.235 2576 -
all-2697 -
obs--100 %
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)
11.6663-0.1537-0.29620.9660.01110.3770.02-0.0872-0.01610.0372-0.0280.01950.04610.01660.0080.01240.0016-0.01240.063-0.00660.073127.07293.539921.8908
21.52020.39720.160.51410.01120.75780.02720.02210.0833-0.0395-0.00930.0289-0.0234-0.0059-0.01790.01050.0107-0.00630.02470.00170.09264.202521.63854.7969
30.4914-0.132-0.09610.4349-0.38710.6802-0.0167-0.04190.0663-0.00370.00730.0359-0.02930.02870.00940.0093-0.0089-0.01520.0459-0.00250.099736.390724.7807-3.143
40.3106-0.01770.0181.0196-0.30180.7006-0.0229-0.0276-0.00370.00780.03170.06070.01960.0038-0.00880.00330.00890.00230.06040.00690.0976-4.8092-4.310624.6416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A467 - 609
2X-RAY DIFFRACTION2B467 - 609
3X-RAY DIFFRACTION3C461 - 609
4X-RAY DIFFRACTION4D461 - 609

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