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- PDB-3g1w: Crystal structure of sugar ABC transporter (sugar-binding protein... -

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Basic information

Entry
Database: PDB / ID: 3g1w
TitleCrystal structure of sugar ABC transporter (sugar-binding protein) from Bacillus halodurans
ComponentsSugar ABC transporter
KeywordsTRANSPORT PROTEIN / Sugar ABC transporter / Sugar-binding protein / Bacillus halodurans / target 11229f / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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
Sugar ABC transporter (Sugar-binding protein)
Similarity search - Component
Biological speciesBacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsZhang, Z. / Eswaramoorthy, S. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of sugar ABC transporter (sugar-binding protein) from Bacillus halodurans.
Authors: Zhang, Z. / Eswaramoorthy, S. / Swaminathan, S. / Burley, S.K.
History
DepositionJan 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 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: Sugar ABC transporter
B: Sugar ABC transporter


Theoretical massNumber of molelcules
Total (without water)67,7212
Polymers67,7212
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-12.2 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.457, 87.864, 113.582
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 Sugar ABC transporter / Sugar-binding protein


Mass: 33860.379 Da / Num. of mol.: 2 / Fragment: UNP residues 42-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Strain: C-125 / DSM 18197 / FERM 7344 / JCM 9153 / Gene: BH3448 / Plasmid: BC-pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K7B8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M Calcium chloride dihydrate, 0.1 M BIS-TRIS pH 6.5, 30% v/v PEG 550, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 21, 2009 / Details: mirrors
RadiationMonochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 33281 / Num. obs: 33281 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 7.5
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.1 / % possible all: 88.4

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.02→33.92 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.949 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines. Program Phenix.refine has also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.23711 1760 5 %RANDOM
Rwork0.19308 ---
obs0.19527 33281 100 %-
all-33281 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.02→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4470 0 0 229 4699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224558
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9476210
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2325578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52625.516223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73915712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3871517
X-RAY DIFFRACTIONr_chiral_restr0.1220.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023527
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.22184
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23170
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3151.52955
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84924607
X-RAY DIFFRACTIONr_scbond_it3.31531835
X-RAY DIFFRACTIONr_scangle_it4.7594.51603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.02→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 93 -
Rwork0.247 1568 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 34.321 Å / Origin y: 42.02 Å / Origin z: 54.056 Å
111213212223313233
T0.0111 Å20.0052 Å2-0.0098 Å2--0.1042 Å2-0.0121 Å2---0.0082 Å2
L0.5421 °20.107 °2-0.1857 °2-0.1666 °20.0545 °2--0.7358 °2
S-0.0153 Å °0.0571 Å °-0.0962 Å °0.0137 Å °0.0251 Å °-0.0109 Å °0.0095 Å °0.0044 Å °-0.0098 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 300
2X-RAY DIFFRACTION1B42 - 300

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