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- PDB-3eki: Structural insights of the Mycoplasma hyorhinis protein Mh-p37: A... -

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Basic information

Entry
Database: PDB / ID: 3eki
TitleStructural insights of the Mycoplasma hyorhinis protein Mh-p37: A putative thiamine pyrophosphate transporter
ComponentsHigh affinity transport system protein p37
KeywordsTPP BINDING PROTEIN / Mycoplasma / p37 / TPP / cell membrane / Lipoprotein / membrane / transport / transport protein / Palmitate / extracytoplasmic thiamine binding lipoprotein / Cypl
Function / homology
Function and homology information


regulation of protein phosphorylation / regulation of cell migration / host cell cytoplasm / plasma membrane
Similarity search - Function
Cypl, domain I / CypI, domain 2 / Extracytoplasmic thiamine-binding lipoprotein / Thiamine-binding lipoprotein, domain I / Extracytoplasmic thiamine-binding lipoprotein, domain II / Extracytoplasmic thiamine-binding lipoprotein / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / THIAMINE DIPHOSPHATE / High affinity transport system protein p37
Similarity search - Component
Biological speciesMycoplasma hyorhinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSippel, K.H. / Robbins, A.H. / Reutzel, R. / McKenna, R.
Citation
Journal: J.Bacteriol. / Year: 2009
Title: Structural insights into the extracytoplasmic thiamine-binding lipoprotein p37 of Mycoplasma hyorhinis
Authors: Sippel, K.H. / Robbins, A.H. / Reutzel, R. / Boehlein, S.K. / Namiki, K. / Goodison, S. / Agbandje-McKenna, M. / Rosser, C.J. / McKenna, R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure determination of the cancer-associated mycoplasma hyorhinis protein Mh-p37
Authors: Sippel, K.H. / Robbins, A.H. / Reutzal, R. / Domsic, J. / Boehlein, S.K. / Govindasamy, L. / Agbandje-McKenna, M. / Rosser, C.J. / McKenna, R.
History
DepositionSep 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 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

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Assembly

Deposited unit
A: High affinity transport system protein p37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,27512
Polymers46,1181
Non-polymers1,15711
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.457, 67.586, 59.838
Angle α, β, γ (deg.)90.00, 106.28, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomeric

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Components

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Protein , 1 types, 1 molecules A

#1: Protein High affinity transport system protein p37


Mass: 46117.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma hyorhinis (bacteria) / Gene: p37 / Plasmid: PET31p37 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P15363

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Non-polymers , 5 types, 333 molecules

#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 298 K / Method: batch / pH: 4
Details: 0.1 M Ammonium Bromide, 0.1 M Citric Acid, 40% PEG 4000, under paraffin oil, pH 4.0, Batch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9169 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2002
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9169 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 49563 / Num. obs: 47500 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.071 / Net I/σ(I): 0.115
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 4759 / Rsym value: 0.288 / % possible all: 95.6

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E78

3e78


Resolution: 1.6→40 Å
Isotropic thermal model: isotropic except for one calcium ion
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflectionSelection details
Rfree0.227 2375 random
Rwork0.183 --
all0.184 49563 -
obs-47500 -
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 41 322 3334
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.024

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