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- PDB-6tct: MakD from the mak operon of Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 6tct
TitleMakD from the mak operon of Vibrio cholerae
ComponentsMakD
KeywordsUNKNOWN FUNCTION / cytotoxin / putative chaperone
Function / homologyUncharacterized protein
Function and homology information
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsPersson, K. / Nagampalli, R. / Heidler, T. / Wai, S.N.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-05009 Sweden
Swedish Research Council2018-02914 Sweden
CitationJournal: To Be Published
Title: MakD from the mak operon of Vibrio cholerae
Authors: Persson, K. / Nagampalli, R. / Heidler, T. / Wai, S.N.
History
DepositionNov 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: MakD
D: MakD
A: MakD
C: MakD


Theoretical massNumber of molelcules
Total (without water)55,9954
Polymers55,9954
Non-polymers00
Water4,738263
1
B: MakD
D: MakD


Theoretical massNumber of molelcules
Total (without water)27,9972
Polymers27,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-13 kcal/mol
Surface area11410 Å2
MethodPISA
2
A: MakD
C: MakD


Theoretical massNumber of molelcules
Total (without water)27,9972
Polymers27,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-14 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.327, 70.886, 185.715
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 35 or resid 37...
21(chain B and (resid 2 through 35 or resid 37...
31(chain C and (resid 2 through 35 or resid 37 through 126))
41(chain D and (resid 2 through 35 or resid 37 through 126))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLYGLY(chain A and (resid 2 through 35 or resid 37...AC2 - 352 - 35
12TRPTRPVALVAL(chain A and (resid 2 through 35 or resid 37...AC37 - 12537 - 125
13LYSLYSGLNGLN(chain A and (resid 2 through 35 or resid 37...AC2 - 1262 - 126
14LYSLYSGLNGLN(chain A and (resid 2 through 35 or resid 37...AC2 - 1262 - 126
15LYSLYSGLNGLN(chain A and (resid 2 through 35 or resid 37...AC2 - 1262 - 126
16LYSLYSGLNGLN(chain A and (resid 2 through 35 or resid 37...AC2 - 1262 - 126
17LYSLYSGLNGLN(chain A and (resid 2 through 35 or resid 37...AC2 - 1262 - 126
18LYSLYSGLNGLN(chain A and (resid 2 through 35 or resid 37...AC2 - 1262 - 126
19LYSLYSGLNGLN(chain A and (resid 2 through 35 or resid 37...AC2 - 1262 - 126
110LYSLYSGLNGLN(chain A and (resid 2 through 35 or resid 37...AC2 - 1262 - 126
111LYSLYSGLNGLN(chain A and (resid 2 through 35 or resid 37...AC2 - 1262 - 126
112LYSLYSGLNGLN(chain A and (resid 2 through 35 or resid 37...AC2 - 1262 - 126
113LYSLYSGLNGLN(chain A and (resid 2 through 35 or resid 37...AC2 - 1262 - 126
21LYSLYSGLYGLY(chain B and (resid 2 through 35 or resid 37...BA2 - 352 - 35
22TRPTRPVALVAL(chain B and (resid 2 through 35 or resid 37...BA37 - 12537 - 125
23LYSLYSGLNGLN(chain B and (resid 2 through 35 or resid 37...BA2 - 1262 - 126
24LYSLYSGLNGLN(chain B and (resid 2 through 35 or resid 37...BA2 - 1262 - 126
25LYSLYSGLNGLN(chain B and (resid 2 through 35 or resid 37...BA2 - 1262 - 126
26LYSLYSGLNGLN(chain B and (resid 2 through 35 or resid 37...BA2 - 1262 - 126
27LYSLYSGLNGLN(chain B and (resid 2 through 35 or resid 37...BA2 - 1262 - 126
28LYSLYSGLNGLN(chain B and (resid 2 through 35 or resid 37...BA2 - 1262 - 126
29LYSLYSGLNGLN(chain B and (resid 2 through 35 or resid 37...BA2 - 1262 - 126
210LYSLYSGLNGLN(chain B and (resid 2 through 35 or resid 37...BA2 - 1262 - 126
211LYSLYSGLNGLN(chain B and (resid 2 through 35 or resid 37...BA2 - 1262 - 126
212LYSLYSGLNGLN(chain B and (resid 2 through 35 or resid 37...BA2 - 1262 - 126
31LYSLYSGLYGLY(chain C and (resid 2 through 35 or resid 37 through 126))CD2 - 352 - 35
32TRPTRPGLNGLN(chain C and (resid 2 through 35 or resid 37 through 126))CD37 - 12637 - 126
41LYSLYSGLYGLY(chain D and (resid 2 through 35 or resid 37 through 126))DB2 - 352 - 35
42TRPTRPGLNGLN(chain D and (resid 2 through 35 or resid 37 through 126))DB37 - 12637 - 126

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Components

#1: Protein
MakD


Mass: 13998.710 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: VC_A0880 / Plasmid: pETHis1a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KL67
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris pH 8.0 60% polypropylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.02→46.63 Å / Num. obs: 37693 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.039 / Rrim(I) all: 0.143 / Net I/σ(I): 11.1 / Num. measured all: 495423 / Scaling rejects: 3
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
2.02-2.0913.91.8145009636050.5960.5041.8841.6100
7.82-46.6311.20.0785757650.9980.0210.07424.899.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.1data scaling
PDB_EXTRACT3.25data extraction
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.02→38.84 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 1415 3.76 %
Rwork0.1872 36187 -
obs0.189 37602 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.05 Å2 / Biso mean: 52.1211 Å2 / Biso min: 23.59 Å2
Refinement stepCycle: final / Resolution: 2.02→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3886 0 0 263 4149
Biso mean---52.2 -
Num. residues----500
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1480X-RAY DIFFRACTION10.195TORSIONAL
12B1480X-RAY DIFFRACTION10.195TORSIONAL
13C1480X-RAY DIFFRACTION10.195TORSIONAL
14D1480X-RAY DIFFRACTION10.195TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.02-2.090.32861370.277235233660100
2.09-2.180.33211400.255835653705100
2.18-2.270.29281390.23235583697100
2.27-2.390.27611400.226635833723100
2.39-2.540.25311400.215535853725100
2.54-2.740.281410.212336023743100
2.74-3.020.27271410.214536073748100
3.02-3.450.23211420.179936343776100
3.45-4.350.18491440.156836833827100
4.35-38.840.21591510.16443847399899
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)
14.52243.33870.64936.3645-0.06233.64960.2193-0.5129-0.62330.2213-0.3752-1.2698-0.02160.40730.08890.2973-0.06090.02030.41430.07290.5082-1.435539.811430.6579
23.64311.30461.26214.02710.10453.5196-0.37620.12260.0316-0.98480.2220.2047-0.3668-0.07820.11550.4312-0.0717-0.0170.2522-0.00120.2384-0.376-2.975217.567
32.0715-0.09841.95332.2054-0.64144.25890.0657-0.0887-0.106-0.51330.0814-0.1945-0.0454-0.3349-0.13240.5296-0.05920.18380.35670.01920.3885-19.247630.011416.0539
43.69951.74571.64285.92691.29774.01850.0626-0.282-0.24370.1018-0.0382-0.5971-0.049-0.10850.01830.1816-0.05270.04380.28210.050.311317.23745.0733.3367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:126)A2 - 126
2X-RAY DIFFRACTION2(chain B and resid 2:126)B2 - 126
3X-RAY DIFFRACTION3(chain C and resid 2:126)C2 - 126
4X-RAY DIFFRACTION4(chain D and resid 2:126)D2 - 126

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