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- PDB-3cyq: The crystal structure of the complex of the C-terminal domain of ... -

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Basic information

Entry
Database: PDB / ID: 3cyq
TitleThe crystal structure of the complex of the C-terminal domain of Helicobacter pylori MotB (residues 125-256) with N-acetylmuramic acid
ComponentsChemotaxis protein motB
KeywordsMEMBRANE PROTEIN / Helicobacter pylori / bacterial flagellar motor / peptidoglycan binding / Bacterial flagellum / Chemotaxis / Flagellar rotation / Inner membrane / Membrane / Transmembrane
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / chemotaxis / identical protein binding / plasma membrane
Similarity search - Function
Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / OmpA-like domain / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-beta-muramic acid / Motility protein B
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsRoujeinikova, A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystal structure of the cell wall anchor domain of MotB, a stator component of the bacterial flagellar motor: implications for peptidoglycan recognition.
History
DepositionApr 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
B: Chemotaxis protein motB
C: Chemotaxis protein motB
D: Chemotaxis protein motB
E: Chemotaxis protein motB
F: Chemotaxis protein motB
G: Chemotaxis protein motB
H: Chemotaxis protein motB
I: Chemotaxis protein motB
A: Chemotaxis protein motB
J: Chemotaxis protein motB
K: Chemotaxis protein motB
L: Chemotaxis protein motB
M: Chemotaxis protein motB
N: Chemotaxis protein motB
O: Chemotaxis protein motB
P: Chemotaxis protein motB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,62618
Polymers255,04016
Non-polymers5872
Water22,9511274
1
B: Chemotaxis protein motB
C: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)31,8802
Polymers31,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Chemotaxis protein motB
E: Chemotaxis protein motB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1733
Polymers31,8802
Non-polymers2931
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Chemotaxis protein motB
J: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)31,8802
Polymers31,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Chemotaxis protein motB
N: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)31,8802
Polymers31,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
O: Chemotaxis protein motB
P: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)31,8802
Polymers31,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
H: Chemotaxis protein motB
I: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)31,8802
Polymers31,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
F: Chemotaxis protein motB
G: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)31,8802
Polymers31,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
K: Chemotaxis protein motB
L: Chemotaxis protein motB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1733
Polymers31,8802
Non-polymers2931
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: Chemotaxis protein motB
J: Chemotaxis protein motB
K: Chemotaxis protein motB
L: Chemotaxis protein motB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0535
Polymers63,7604
Non-polymers2931
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24450 Å2
ΔGint-29.4 kcal/mol
Surface area5920 Å2
MethodPISA
10
B: Chemotaxis protein motB
C: Chemotaxis protein motB
D: Chemotaxis protein motB
E: Chemotaxis protein motB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0535
Polymers63,7604
Non-polymers2931
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24220 Å2
ΔGint-27.9 kcal/mol
Surface area6030 Å2
MethodPISA
11
M: Chemotaxis protein motB
N: Chemotaxis protein motB
O: Chemotaxis protein motB
P: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)63,7604
Polymers63,7604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23990 Å2
ΔGint-31.2 kcal/mol
Surface area5790 Å2
MethodPISA
12
F: Chemotaxis protein motB
G: Chemotaxis protein motB
H: Chemotaxis protein motB
I: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)63,7604
Polymers63,7604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23880 Å2
ΔGint-26.6 kcal/mol
Surface area5880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.781, 110.058, 113.664
Angle α, β, γ (deg.)90.000, 104.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chemotaxis protein motB / / Motility protein B


Mass: 15939.984 Da / Num. of mol.: 16 / Fragment: C-terminal domain, UNP residues 126-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: motB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P56427
#2: Sugar ChemComp-AMU / N-acetyl-beta-muramic acid / N-acetyl-muramic acid / BETA-N-ACETYLMURAMIC ACID / N-Acetylmuramic acid


Type: D-saccharide, beta linking / Mass: 293.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO8
IdentifierTypeProgram
b-D-GlcpNAc3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
MurNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1274 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 100 mM Tris/HCl, 16-18% PEG 3350, 200 mM sodium tartrate, 10 mM N-acetylmuramic acid, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→109.76 Å / Num. obs: 103524 / % possible obs: 96 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 7
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.8 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.935 / SU B: 15.97 / SU ML: 0.201 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.446 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.289 5187 5 %RANDOM
Rwork0.217 ---
obs0.22 103503 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.046 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20.22 Å2
2--0.17 Å20 Å2
3---1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17110 0 40 1274 18424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02217537
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211929
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.94723745
X-RAY DIFFRACTIONr_angle_other_deg1.092329029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21752115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05624.362917
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.952153036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4115129
X-RAY DIFFRACTIONr_chiral_restr0.0820.22637
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023593
X-RAY DIFFRACTIONr_nbd_refined0.2080.24127
X-RAY DIFFRACTIONr_nbd_other0.1890.212767
X-RAY DIFFRACTIONr_nbtor_refined0.180.28530
X-RAY DIFFRACTIONr_nbtor_other0.0890.29235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.21010
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0330.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.263
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.2112
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.222
X-RAY DIFFRACTIONr_mcbond_it3.621613735
X-RAY DIFFRACTIONr_mcbond_other1.05464198
X-RAY DIFFRACTIONr_mcangle_it4.246817374
X-RAY DIFFRACTIONr_scbond_it4.8787805
X-RAY DIFFRACTIONr_scangle_it6.461126371
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 407 -
Rwork0.266 7408 -
all-7815 -
obs--97.75 %
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)
11.7561-0.24690.11361.9488-0.33391.11220.1070.1903-0.23310.02390.0161-0.15170.07970.0585-0.123-0.05490.01390.0027-0.1422-0.01090.018859.963-12.361-5.295
21.7084-0.1116-0.15372.7247-1.1512.05410.0911-0.18390.3320.1796-0.1022-0.389-0.24460.28790.0112-0.0673-0.04070.0144-0.1227-0.02320.064360.1411.5864.704
31.3995-0.0213-0.15713.43240.06011.69230.0044-0.0947-0.01420.20080.06040.06260.0392-0.1445-0.0648-0.06660.00850.0494-0.08990.0139-0.085136.635-1.64512.449
41.8982-0.2489-0.42354.63660.28282.41130.0920.2885-0.0355-0.4212-0.01940.3696-0.1163-0.3982-0.0726-0.07810.0362-0.0266-0.0470.0007-0.074736.4841.475-13.036
52.3397-0.02140.10083.1498-0.33941.33380.0502-0.2713-0.00090.2549-0.00180.064-0.05830.1075-0.0484-0.0942-0.02370.0161-0.0945-0.0153-0.042914.20752.72112.825
61.3969-0.26280.02374.0281-0.48022.6538-0.01310.1965-0.0228-0.39020.0531-0.27850.13030.303-0.0399-0.10130.00390.0376-0.0857-0.0298-0.051714.51949.999-13.065
71.62290.03210.052.04350.33720.67560.05020.1930.12860.0149-0.04810.2121-0.0961-0.0248-0.0021-0.09870.034-0.0031-0.1331-0.02950.0459-8.83363.499-5.247
82.5015-0.04050.3952.80451.37312.75120.1313-0.3056-0.44580.1185-0.15790.50420.1767-0.35690.0265-0.1498-0.0571-0.0032-0.1530.02960.1721-9.40639.7054.455
91.5651-0.12930.03221.5631-0.45471.39050.07610.18-0.2589-0.02090.0131-0.1850.12610.0708-0.0891-0.0660.0223-0.0011-0.1255-0.01710.033574.278-12.302-60.325
101.9475-0.1716-0.30132.5984-1.23232.15860.0607-0.17980.33050.1602-0.0859-0.3145-0.23940.3240.0253-0.0806-0.04710.0152-0.1171-0.02360.057574.50311.693-50.1
111.38380.0747-0.24213.4427-0.01471.63880.0189-0.1439-0.02270.23520.03380.00670.0418-0.1067-0.0528-0.05520.01610.0548-0.08690.0256-0.086750.936-1.589-42.565
121.6171-0.4007-0.09714.5740.11072.20770.08190.2391-0.0023-0.45950.0130.3319-0.0824-0.3361-0.0949-0.08930.0266-0.0245-0.04880.0252-0.058850.8241.54-68.042
132.210.2820.11183.8439-0.12081.36420.0614-0.25820.02690.23760.01070.0658-0.07760.1204-0.0722-0.1134-0.01230.0105-0.0773-0.0245-0.065328.51952.771-42.16
141.6587-0.35960.18374.4153-0.32272.4222-0.06580.1987-0.0821-0.35520.0683-0.23870.07020.2863-0.0025-0.0998-0.00290.0653-0.096-0.0233-0.052528.83350.073-68.065
152.1007-0.1762-0.00741.93240.4711.42450.05320.21670.1636-0.0687-0.02160.1471-0.1294-0.0793-0.0316-0.10080.01830.0067-0.157-0.01140.04395.46763.56-60.245
162.32910.06760.71543.15951.42672.71920.1776-0.3206-0.44950.0753-0.1270.42410.1946-0.3033-0.0506-0.1418-0.0534-0.009-0.15290.04590.12814.9239.778-50.564
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BA119 - 2511 - 133
2X-RAY DIFFRACTION2CB119 - 2511 - 133
3X-RAY DIFFRACTION3DC119 - 2501 - 132
4X-RAY DIFFRACTION4ED119 - 2501 - 132
5X-RAY DIFFRACTION5FE119 - 2511 - 133
6X-RAY DIFFRACTION6GF119 - 2521 - 134
7X-RAY DIFFRACTION7HG119 - 2501 - 132
8X-RAY DIFFRACTION8IH119 - 2501 - 132
9X-RAY DIFFRACTION9AI119 - 2511 - 133
10X-RAY DIFFRACTION10JJ119 - 2521 - 134
11X-RAY DIFFRACTION11KK119 - 2501 - 132
12X-RAY DIFFRACTION12LL119 - 2501 - 132
13X-RAY DIFFRACTION13MM119 - 2511 - 133
14X-RAY DIFFRACTION14NN119 - 2521 - 134
15X-RAY DIFFRACTION15OO119 - 2501 - 132
16X-RAY DIFFRACTION16PP119 - 2501 - 132

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