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- PDB-3e78: Structure determination of the cancer-associated Mycoplasma hyorh... -

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Basic information

Entry
Database: PDB / ID: 3.0E+78
TitleStructure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37
ComponentsHigh affinity transport system protein p37
KeywordsTPP Binding Protein / Mycoplasma / p37 / TPP / Cell membrane / Lipoprotein / Membrane / Palmitate / Transport
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
THIAMINE DIPHOSPHATE / High affinity transport system protein p37
Similarity search - Component
Biological speciesMycoplasma hyorhinis (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.9 Å
AuthorsSippel, K.H. / Robbins, A.H. / Reutzel, R. / Domsic, J. / McKenna, R.
Citation
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. / Reutzel, R. / Domsic, J. / Boehlein, S.K. / Govindasamy, L. / Agbandje-McKenna, M. / Rosser, C.J. / McKenna, R.
#1: Journal: To be Published
Title: A magic triangle for experimental phasing of macromolecules
Authors: Beck, T. / Krasauskas, A. / Gruene, T. / Sheldrick, G.M.
History
DepositionAug 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)46,6194
Polymers46,1181
Non-polymers5013
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.445, 68.761, 60.024
Angle α, β, γ (deg.)90.00, 108.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 298 K / Method: batch / pH: 3
Details: 0.1 M Ammonium Bromide, O.1 M Citric Acid, 40% PEG 4000, 9% N-decyl-beta-D-maltoside detergent , pH 3.0, Batch, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 2008 / Details: Osmic mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 29894 / % possible obs: 96.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 26.427 Å2 / Rsym value: 0.067 / Net I/σ(I): 16.3
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 5 / Num. unique all: 2860 / Rsym value: 0.376 / % possible all: 93.2

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Processing

Software
NameClassification
CrystalCleardata collection
SHELXEmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1495 -Random
obs0.186 29894 96.2 %-
Displacement parametersBiso mean: 32.694 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 28 147 3152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_bond_d0.006

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