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- PDB-3l49: CRYSTAL STRUCTURE OF ABC SUGAR TRANSPORTER SUBUNIT FROM Rhodobact... -

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Basic information

Entry
Database: PDB / ID: 3l49
TitleCRYSTAL STRUCTURE OF ABC SUGAR TRANSPORTER SUBUNIT FROM Rhodobacter sphaeroides 2.4.1
ComponentsABC sugar (Ribose) transporter, periplasmic substrate-binding subunit
KeywordsTRANSPORT PROTEIN / SUGAR BINDING/TRANSPORTER / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NYSGRC / UNKNOWN LIGAND / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


cell envelope / carbohydrate binding
Similarity search - Function
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
Unknown ligand / Monosaccharide ABC transporter substrate-binding protein, CUT2 family
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPatskovsky, Y. / Ozyurt, S. / Dickey, M. / Do, J. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York Structural GenomiX Research Consortium (NYSGXRC) / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF ABC SUGAR TRANSPORTER FROM Rhodobacter sphaeroides
Authors: Patskovsky, Y. / Ozyurt, S. / Dickey, M. / Do, J. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionDec 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 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 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC sugar (Ribose) transporter, periplasmic substrate-binding subunit
B: ABC sugar (Ribose) transporter, periplasmic substrate-binding subunit
C: ABC sugar (Ribose) transporter, periplasmic substrate-binding subunit
D: ABC sugar (Ribose) transporter, periplasmic substrate-binding subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,1308
Polymers00
Non-polymers126,1308
Water4,035224
1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5322
Polymers00
Non-polymers31,5322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5322
Polymers00
Non-polymers31,5322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5322
Polymers00
Non-polymers31,5322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5322
Polymers00
Non-polymers31,5322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0654
Polymers00
Non-polymers63,0654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-13 kcal/mol
Surface area21750 Å2
MethodPISA
6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0654
Polymers00
Non-polymers63,0654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-11 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.310, 75.712, 77.438
Angle α, β, γ (deg.)106.41, 115.49, 96.71
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12I
22K
32H
42L
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
ABC sugar (Ribose) transporter, periplasmic substrate-binding subunit / PERIPLASMIC SUGAR BINDING PROTEIN


Mass: 31532.451 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RHOS4_09560, RSP_2365 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3J3W0
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 200MM SODIUM ACETATE, PH 4.6, 100MM TRIS-HCL, PH 8.5, 10% GLYCEROL, 30% PEG4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 12, 2009 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 56552 / % possible obs: 99.8 % / Observed criterion σ(I): -5 / Redundancy: 3.9 % / Biso Wilson estimate: 31.58 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 3.5
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.404 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25436 1661 3.1 %RANDOM
Rwork0.19321 ---
obs0.19504 52491 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.962 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å2-0.25 Å2-0.43 Å2
2--1.45 Å2-0.27 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8608 0 40 224 8872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228826
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.95812062
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79351142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.0526.097392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.859151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7621530
X-RAY DIFFRACTIONr_chiral_restr0.0890.21397
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026760
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1480.34226
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.56092
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.5642
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.356
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6525758
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.51139122
X-RAY DIFFRACTIONr_scbond_it8.15133428
X-RAY DIFFRACTIONr_scangle_it11.12552931
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
210tight positional0.240.1
210tight positional0.390.01
210tight positional0.290
210tight positional0.810
12097medium positional0.40.5
12097medium positional0.40
12097medium positional0.390
12097medium positional0.390
210tight thermal5.025
210tight thermal5.820.5
210tight thermal7.360.05
210tight thermal5.910
12097medium thermal5.645
12097medium thermal5.440
12097medium thermal5.340
12097medium thermal5.810
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 114 -
Rwork0.262 3660 -
obs--90.4 %

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