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- PDB-5bq3: Crystal structure of a sugar ABC transporter (ACTODO_00688) from ... -

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Basic information

Entry
Database: PDB / ID: 5bq3
TitleCrystal structure of a sugar ABC transporter (ACTODO_00688) from Actinomyces odontolyticus ATCC 17982 at 2.60 A resolution
ComponentsRhamnose ABC transporter, rhamnose-binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


rhamnose transmembrane transport / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
Rhamnose ABC transporter, substrate-binding protein RhaS / Autoinducer 2 ABC transporter, substrate-binding protein LsrB / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Autoinducer 2-binding protein LsrB
Similarity search - Component
Biological speciesActinomyces odontolyticus ATCC 17982 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a sugar ABC transporter (ACTODO_00688) from Actinomyces odontolyticus ATCC 17982 at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhamnose ABC transporter, rhamnose-binding protein
B: Rhamnose ABC transporter, rhamnose-binding protein
C: Rhamnose ABC transporter, rhamnose-binding protein
D: Rhamnose ABC transporter, rhamnose-binding protein


Theoretical massNumber of molelcules
Total (without water)139,2144
Polymers139,2144
Non-polymers00
Water4,179232
1
A: Rhamnose ABC transporter, rhamnose-binding protein


Theoretical massNumber of molelcules
Total (without water)34,8041
Polymers34,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rhamnose ABC transporter, rhamnose-binding protein


Theoretical massNumber of molelcules
Total (without water)34,8041
Polymers34,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Rhamnose ABC transporter, rhamnose-binding protein


Theoretical massNumber of molelcules
Total (without water)34,8041
Polymers34,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Rhamnose ABC transporter, rhamnose-binding protein


Theoretical massNumber of molelcules
Total (without water)34,8041
Polymers34,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.780, 83.280, 104.220
Angle α, β, γ (deg.)90.000, 111.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Rhamnose ABC transporter, rhamnose-binding protein


Mass: 34803.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomyces odontolyticus ATCC 17982 (bacteria)
Gene: rhaS, ACTODO_00688 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7BAM4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (22-352) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (22-352) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium sulfate, 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9116,0.9796
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2015
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91161
20.97961
ReflectionResolution: 2.6→19.936 Å / Num. obs: 40255 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 1.553 % / Biso Wilson estimate: 67.351 Å2 / Rmerge F obs: 0.989 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.137 / Net I/σ(I): 6.47 / Num. measured all: 117477
Reflection shell
Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
2.6-2.670.3450.92719122610757821.306194.7
2.67-2.740.4760.7471.28627582455161.05394.7
2.74-2.820.5730.5981.58328571553630.84393.8
2.82-2.910.6320.5371.78080558752240.75893.5
2.91-30.7380.4012.27507531348990.56692.2
3-3.110.810.3112.76733520546750.4489.8
3.11-3.220.8330.2553.57304506046990.3692.9
3.22-3.360.8980.1914.77178482045340.2794.1
3.36-3.510.9510.1316.36895463343790.18594.5
3.51-3.680.9560.1097.56511442641490.15493.7
3.68-3.880.9790.08396209424039930.11894.2
3.88-4.110.990.06210.15166395435630.08790.1
4.11-4.390.9880.05911.75642374935270.08494.1
4.39-4.750.9910.04614.25224347932550.06593.6
4.75-5.20.9940.04413.94751322330110.06293.4
5.2-5.810.9920.05211.94059287626500.07392.1
5.81-6.710.9920.04713.23505255322850.06689.5
6.71-8.220.9950.03416.63262216820010.04992.3
8.22-11.630.9970.02620.42326167715030.03689.6
11.63-19.9360.9960.02921.210489106580.0472.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALENovember 3, 2014 BUILT=20141118data scaling
SHELXphasing
SHARPphasing
BUSTER2.10.2refinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→19.936 Å / Cor.coef. Fo:Fc: 0.9244 / Cor.coef. Fo:Fc free: 0.9097 / Occupancy max: 1 / Occupancy min: 0.75 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: 1. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT 5. NCS RESTRAINTS WERE APPLIED DURING REFINEMENT USING LSSR (-AUTONCS) IN BUSTER. 6. DENSITY FOR CHAIN D IS POORER THAN THE OTHER THREE CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 2018 5.01 %RANDOM
Rwork0.207 ---
obs0.2076 40251 96.88 %-
Displacement parametersBiso max: 219.42 Å2 / Biso mean: 70.7567 Å2 / Biso min: 21.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.1527 Å20 Å26.2098 Å2
2--2.8603 Å20 Å2
3----5.013 Å2
Refine analyzeLuzzati coordinate error obs: 0.425 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9217 0 0 232 9449
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4310SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes289HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1366HARMONIC5
X-RAY DIFFRACTIONt_it9361HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1270SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10718SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9361HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg12706HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion1.9
X-RAY DIFFRACTIONt_other_torsion2.63
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2837 160 5.24 %
Rwork0.2403 2893 -
all0.2426 3053 -
obs--96.88 %
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)
11.08810.71060.20443.77650.4710.90990.0367-0.06060.04080.1726-0.0686-0.1076-0.037-0.00440.0319-0.137-0.00010.0107-0.0690.0148-0.08137.049610.66813.0686
21.54710.3664-0.31695.2009-0.28150.5849-0.0876-0.2328-0.04110.49880.0994-0.22230.0210.0593-0.0118-0.1830.06230.06-0.09170.0513-0.079535.4034-9.434913.1996
31.37280.36960.17896.7147-0.81691.20150.1529-0.41690.01870.6077-0.0553-0.0528-0.0587-0.2142-0.0976-0.03180.0098-0.074-0.1282-0.0046-0.31468.33284.358445.3368
41.10870.62830.27752.52232.20041.14510.0520.1246-0.04860.33650.4971-0.29360.05870.6056-0.5491-0.29860.0206-0.06450.0014-0.1555-0.0158-21.841731.390127.9544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|40 - 352}A40 - 352
2X-RAY DIFFRACTION2{B|40 - 352}B40 - 352
3X-RAY DIFFRACTION3{C|41 - 352}C41 - 352
4X-RAY DIFFRACTION4{D|41 - 352}D41 - 352

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