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- PDB-3myu: Mycoplasma genitalium MG289 -

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Basic information

Entry
Database: PDB / ID: 3myu
TitleMycoplasma genitalium MG289
ComponentsHigh affinity transport system protein p37
KeywordsVIB BINDING PROTEIN / MYCOPLASMA / MYCOPLASMA GENITALIUM / MG289 / P37 / G37 / CYPL / EXTRACYTOPLASMIC / THIAMINE BINDING PROTEIN / LIPOPROTEIN / ATP BINDING CASSETTE TRANSPORTER BINDING PROTEIN
Function / homology
Function and homology information


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
ACETATE ION / Chem-VIB / High affinity transport system protein p37
Similarity search - Component
Biological speciesMycoplasma genitalium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSippel, K.H. / Boehlein, S.K. / Govindasamy, L. / Namiki, K. / Satai, Y. / Quirit, J.G. / Agbandje-McKenna, M. / Goodison, S. / Rosser, C.J. / Sankaran, B. / McKenna, R.
Citation
Journal: Proteins / Year: 2011
Title: Insights into Mycoplasma genitalium metabolism revealed by the structure of MG289, an extracytoplasmic thiamine binding lipoprotein.
Authors: Sippel, K.H. / Venkatakrishnan, B. / Boehlein, S.K. / Sankaran, B. / Quirit, J.G. / Govindasamy, L. / Agbandje-McKenna, M. / Goodison, S. / Rosser, C.J. / McKenna, R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Cloning, expression, purification, crystallization and preliminary X-ray analysis of Mycoplasma genitalium protein MG289.
Authors: Sippel, K.H. / Boehlein, S.K. / Sakai, Y. / Quirit, J.G. / Agbandje-McKenna, M. / Rosser, C.J. / McKenna, R.
#2: 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.
#3: 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.
History
DepositionMay 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
B: High affinity transport system protein p37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7546
Polymers79,1052
Non-polymers6494
Water4,450247
1
A: High affinity transport system protein p37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9364
Polymers39,5531
Non-polymers3833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: High affinity transport system protein p37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8182
Polymers39,5531
Non-polymers2651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.279, 90.366, 175.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein High affinity transport system protein p37


Mass: 39552.562 Da / Num. of mol.: 2 / Fragment: N-TERMINAL TRUNCATION (DELTA 1-25) / Mutation: S26M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium (bacteria) / Strain: G37 / Gene: MG289, p37 / Plasmid: pET31f1m1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q49410
#2: Chemical ChemComp-VIB / 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM / THIAMIN / VITAMIN B1


Mass: 265.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N4OS
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 298 K / pH: 4.6
Details: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE TRIHYDRATE pH 4.6 and 15% PEG 4000 AND HAMPTON SILVER BULLET BIO CONDITION 49, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2009
Details: VERTICALLY COLLIMATING PREMIRROR, LN2 COOLED DOUBLE- CRYSTAL SILICON (111) MONOCHROMATOR, TOROIDAL FOCUSING M2 MIRROR
RadiationMonochromator: LIQUID NITROGEN COOLED DUAL SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→45.18 Å / Num. obs: 52800 / % possible obs: 90.9 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 22
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.56 / % possible all: 90

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(AutoMR: 1.6.1_348)model building
PHENIX(phenix.refine: 1.6.1_348)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(AUTOMR: 1.6.1_348)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EKI

3eki


Resolution: 1.95→45.18 Å / SU ML: 0.22 / σ(F): 0.11 / Phase error: 28.39 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2553 2000 3.79 %
Rwork0.2209 --
obs0.2222 52800 90.94 %
all-58060 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.809 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso mean: 38.96 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5447 0 44 247 5738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065648
X-RAY DIFFRACTIONf_angle_d0.9387642
X-RAY DIFFRACTIONf_dihedral_angle_d14.0492084
X-RAY DIFFRACTIONf_chiral_restr0.061811
X-RAY DIFFRACTIONf_plane_restr0.004985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9505-2.02020.34611530.28183896X-RAY DIFFRACTION71
2.0202-2.10110.3251750.26424435X-RAY DIFFRACTION81
2.1011-2.19670.29861890.24194800X-RAY DIFFRACTION87
2.1967-2.31250.29191940.24334950X-RAY DIFFRACTION89
2.3125-2.45740.27052020.24185098X-RAY DIFFRACTION92
2.4574-2.64710.26982070.24495262X-RAY DIFFRACTION95
2.6471-2.91350.25982120.24655405X-RAY DIFFRACTION97
2.9135-3.3350.28522170.2335477X-RAY DIFFRACTION98
3.335-4.20120.22992200.20345612X-RAY DIFFRACTION99
4.2012-45.19510.2152310.18655865X-RAY DIFFRACTION99

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