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- PDB-3tmg: Crystal structure of Glycine betaine, L-proline ABC transporter, ... -

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Basic information

Entry
Database: PDB / ID: 3tmg
TitleCrystal structure of Glycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein (ProX) from Borrelia burgdorferi
ComponentsGlycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein (ProX)Trimethylglycine
KeywordsTRANSPORT PROTEIN / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
Glycine betaine-binding periplasmic protein; domain 2 / ABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIMETHYL GLYCINE / Unknown ligand / Glycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Glycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein (ProX) from Borrelia burgdorferi
Authors: SSGCID / Gardberg, A. / Fox, D. / Staker, B. / Stewart, L.
History
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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
A: Glycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein (ProX)
B: Glycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein (ProX)
C: Glycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein (ProX)
D: Glycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein (ProX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,74111
Polymers127,1444
Non-polymers5977
Water14,772820
1
A: Glycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein (ProX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9663
Polymers31,7861
Non-polymers1802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein (ProX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9042
Polymers31,7861
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein (ProX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9663
Polymers31,7861
Non-polymers1802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein (ProX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9043
Polymers31,7861
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.400, 56.750, 107.060
Angle α, β, γ (deg.)92.300, 102.400, 105.250
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glycine betaine, L-proline ABC transporter, glycine/betaine/L-proline-binding protein (ProX) / Trimethylglycine


Mass: 31786.119 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: BB_0144 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O51169
#2: Chemical
ChemComp-BET / TRIMETHYL GLYCINE / Trimethylglycine


Mass: 118.154 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12NO2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 820 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: EBS internal tracking number 220361B9.PACT B9: 0.2 M LiCl, 0.1 M MES pH 6, 20% PEG 6000. BobuA.17327.a.A2 PW31644 at 26 mg/mL, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 7, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→49.16 Å / Num. all: 91173 / Num. obs: 88358 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 26.791 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 17.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.953.90.4473.625415651295.7
1.95-20.3415.124349624996
2-2.060.294623858614596.1
2.06-2.120.267.323302598396.2
2.12-2.190.214922758584496.4
2.19-2.270.20410.521925561496.7
2.27-2.360.17212.121059540296.7
2.36-2.450.1461420358522997
2.45-2.560.12515.819522503197.1
2.56-2.690.10818.218782482997.1
2.69-2.830.12320.918057457697.6
2.83-30.11323.917345438097.4
3-3.210.0927.816029405597.6
3.21-3.470.06732.615103383297.9
3.47-3.80.05236.213738350597.8
3.8-4.250.03639.512221316197.8
4.25-4.910.03240.910769280698.2
4.91-6.010.03539.59071238298.6
6.01-8.50.03439.56872184098.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Translation2.5 Å49.16 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
MD2data collection
XDSdata reduction
RefinementMethod to determine structure: molecular replacement / Resolution: 1.9→49.16 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.83 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4426 5 %RANDOM
Rwork0.175 ---
obs0.177 88358 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.682 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.37 Å2-0.85 Å2
2---0.32 Å2-0.92 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8366 0 41 820 9227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.028702
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.95611870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40351089
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02825380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58151392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.511515
X-RAY DIFFRACTIONr_chiral_restr0.1050.21301
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216639
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 302 -
Rwork0.241 6182 -
all-6484 -
obs--95.41 %
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)
11.5587-0.03020.55361.05580.05681.6511-0.15730.0144-0.0038-0.09940.0252-0.1006-0.0591-0.06270.13210.05910.00820.02390.0174-0.01240.03621.18112.142-39.116
20.78910.3091-0.00980.51360.08781.27290.0323-0.05490.0166-0.0364-0.03960.0084-0.03430.0550.00720.03070.0358-0.01270.0688-0.03240.05881.93220.995-12.115
31.18190.0777-0.09780.62690.40841.24270.08710.04340.03390.0192-0.1410.0443-0.004-0.09090.05390.04070.01820.00410.0618-0.01930.01248.60746.56638.394
41.1039-0.3984-0.3710.86480.6061.3319-0.00550.01770.07020.02820.0987-0.08520.1832-0.0146-0.09320.0808-0.0210.00820.0251-0.01010.02071.61533.4314.007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 290
2X-RAY DIFFRACTION2B26 - 290
3X-RAY DIFFRACTION3C26 - 290
4X-RAY DIFFRACTION4D26 - 290

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