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- PDB-3imp: New crystal form of the C-terminal domain of Helicobacter pylori ... -

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Basic information

Entry
Database: PDB / ID: 3imp
TitleNew crystal form of the C-terminal domain of Helicobacter pylori MotB (residues 125-256)
ComponentsChemotaxis protein motB
KeywordsMEMBRANE PROTEIN / PEPTIDOGLYCAN BINDING / BACTERIAL FLAGELLUM / CHEMOTAXIS / FLAGELLAR ROTATION / INNER MEMBRANE / MEMBRANE / TRANSMEMBRANE / Cell inner membrane / Cell membrane
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
NICKEL (II) ION / Motility protein B
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRoujeinikova, A.
CitationJournal: Plos One / Year: 2011
Title: Crystallographic and Molecular Dynamics Analysis of Loop Motions Unmasking the Peptidoglycan-Binding Site in Stator Protein MotB of Flagellar Motor
Authors: Reboul, C.F. / Andrews, D.A. / Nahar, M.F. / Buckle, A.M. / Roujeinikova, A.
History
DepositionAug 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
A: Chemotaxis protein motB
F: Chemotaxis protein motB
G: Chemotaxis protein motB
H: Chemotaxis protein motB
I: Chemotaxis protein motB
J: Chemotaxis protein motB
K: Chemotaxis protein motB
L: Chemotaxis protein motB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,53918
Polymers191,28012
Non-polymers2596
Water7,800433
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


Theoretical massNumber of molelcules
Total (without water)31,8802
Polymers31,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Chemotaxis protein motB
F: 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
G: Chemotaxis protein motB
H: Chemotaxis protein motB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0105
Polymers31,8802
Non-polymers1303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: 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
6
K: Chemotaxis protein motB
L: Chemotaxis protein motB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0105
Polymers31,8802
Non-polymers1303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21650 Å2
ΔGint-181.1 kcal/mol
Surface area69390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.560, 100.336, 108.490
Angle α, β, γ (deg.)90.000, 119.510, 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.: 12 / 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 / Plasmid: PET151-D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P56427
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15% PEG3350, 200mM sodium tartrate, 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: 2.5→15 Å / Num. obs: 69194 / % possible obs: 99 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.4
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2.8 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CYP

3cyp


Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.848 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.483 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3498 5.1 %RANDOM
Rwork0.186 ---
obs0.189 69176 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.06 Å2 / Biso mean: 51.788 Å2 / Biso min: 9.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å21.25 Å2
2---0.7 Å20 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12781 0 6 433 13220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02213044
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.94717657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06251574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24124.378683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.964152267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2761596
X-RAY DIFFRACTIONr_chiral_restr0.10.21958
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210056
X-RAY DIFFRACTIONr_nbd_refined0.2230.26263
X-RAY DIFFRACTIONr_nbtor_refined0.3120.29019
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2677
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.27
X-RAY DIFFRACTIONr_mcbond_it0.7081.58161
X-RAY DIFFRACTIONr_mcangle_it1.191212953
X-RAY DIFFRACTIONr_scbond_it1.8935404
X-RAY DIFFRACTIONr_scangle_it2.8224.54704
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 250 -
Rwork0.254 4857 -
all-5107 -
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)
12.69840.6550.71643.0409-0.15174.51570.0825-0.0868-0.06060.1293-0.03970.19180.4781-0.3279-0.0427-0.0828-0.12670.0113-0.0246-0.0055-0.144216.284-11.22332.333
21.89910.22631.52282.21481.055.4803-0.09440.1826-0.2991-0.10040.117-0.43330.56020.4638-0.0226-0.05340.00920.082-0.0298-0.0208-0.080936.99-12.51116.796
33.17820.8523-0.88043.2006-0.06474.78730.1137-0.13380.05980.1706-0.1085-0.1562-0.52380.3566-0.0053-0.0735-0.13-0.048-0.0390.0018-0.151637.59310.9932.351
41.93960.1116-1.52742.5751-0.92826.143-0.08880.15640.2191-0.13910.06270.4044-0.5343-0.39570.0261-0.06560.0146-0.1206-0.04720.0288-0.062617.06912.24516.806
54.3861-1.15320.45965.07250.35463.71230.1081-0.3606-0.62211.16970.3801-0.60110.8543-0.0074-0.48820.2070.0915-0.453-0.22110.01990.06115.274-8.223-11.812
66.96712.02940.5264.7172-0.13323.66480.26010.8318-0.9113-0.34910.2744-0.67340.59980.0739-0.5345-0.08950.0969-0.1199-0.0735-0.1814-0.02380.8-6.633-37.181
74.14140.34221.17762.88190.18424.3260.08990.2370.3456-0.1162-0.0977-0.3308-0.55920.11840.0078-0.10450.03130.009-0.09950.0285-0.06589.12218.455-27.307
83.5441-0.0921.9193.8969-0.04184.47990.0405-0.533-0.06970.35150.04180.3646-0.136-0.3682-0.0824-0.14840.07210.03780.02520.0176-0.1274-13.70411.961-16.939
94.5119-0.5866-0.73654.8416-0.33533.68320.1724-0.38360.6771.27910.34140.5911-0.91860.0894-0.51380.14190.07430.4685-0.3066-0.03450.056248.5238.037-11.682
106.40182.5415-0.85115.73460.24143.61480.31610.86661.0527-0.34580.2660.6973-0.6196-0.1607-0.5821-0.11650.1110.1256-0.05130.184-0.027352.8276.432-37.019
114.57710.6184-1.90872.9386-0.50474.9056-0.00290.2797-0.3426-0.1218-0.07380.34990.4698-0.12530.0767-0.08260.0312-0.0597-0.0921-0.0483-0.044844.447-18.711-27.311
123.4317-0.1634-2.29614.31870.34144.27010.0706-0.46960.08330.36170.0682-0.47890.16040.3372-0.1387-0.12220.0823-0.08090.0135-0.023-0.106967.333-12.178-16.909
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B119 - 251
2X-RAY DIFFRACTION2C119 - 251
3X-RAY DIFFRACTION3D119 - 250
4X-RAY DIFFRACTION4E119 - 250
5X-RAY DIFFRACTION5A119 - 249
6X-RAY DIFFRACTION6F119 - 251
7X-RAY DIFFRACTION7G119 - 250
8X-RAY DIFFRACTION8H119 - 250
9X-RAY DIFFRACTION9I119 - 250
10X-RAY DIFFRACTION10J119 - 250
11X-RAY DIFFRACTION11K119 - 250
12X-RAY DIFFRACTION12L119 - 250

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