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- PDB-3e79: Structure determination of the cancer-associated Mycoplasma hyorh... -

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Basic information

Entry
Database: PDB / ID: 3.0E+79
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
Chem-I3C / 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)47,7366
Polymers46,1181
Non-polymers1,6195
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.107, 69.149, 60.297
Angle α, β, γ (deg.)90.00, 106.81, 90.00
Int Tables number4
Space group name H-MP1211

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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, 186 molecules

#2: Chemical ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H4I3NO4
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


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


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


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


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
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. Crystal soaked in final concentration 0.7mM 5-amino-2,4,6-triiodoisophthalic acid, 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: Jun 18, 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→50 Å / Num. obs: 29985 / % possible obs: 92.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 26.427 Å2 / Rsym value: 0.098 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 2895 / Rsym value: 0.379 / % possible all: 87

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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→50 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
Rfree0.244 1499 -RANDOM
obs0.189 29985 87 %-
Displacement parametersBiso mean: 27.193 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 60 181 3218
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_bond_d0.006

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