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- PDB-3lkb: Crystal structure of a branched chain amino acid ABC transporter ... -

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Entry
Database: PDB / ID: 3lkb
TitleCrystal structure of a branched chain amino acid ABC transporter from Thermus thermophilus with bound valine
ComponentsProbable branched-chain amino acid ABC transporter, amino acid binding protein
KeywordsTRANSPORT PROTEIN / branched amino acid / ABC transporter / 11235g / PSI-II / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / VALINE / Probable branched-chain amino acid ABC transporter, amno acid binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a branched chain amino acid ABC transporter from Thermus thermophilus with bound valine
Authors: Agarwal, R. / Sauder, J.M. / Burley, S.K. / Swaminathan, S.
History
DepositionJan 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable branched-chain amino acid ABC transporter, amino acid binding protein
B: Probable branched-chain amino acid ABC transporter, amino acid binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9858
Polymers86,5842
Non-polymers4006
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable branched-chain amino acid ABC transporter, amino acid binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4924
Polymers43,2921
Non-polymers2003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Probable branched-chain amino acid ABC transporter, amino acid binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4924
Polymers43,2921
Non-polymers2003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.708, 83.176, 122.002
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 Probable branched-chain amino acid ABC transporter, amino acid binding protein


Mass: 43292.062 Da / Num. of mol.: 2 / Fragment: sequence database residues 25-407 / Mutation: V315A, S317A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0451 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 codon+(RIL) / References: UniProt: Q5SL42
#2: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes, 1.4M Sodium citrate, 6% 2-propanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2010 / Details: mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 31204 / Num. obs: 31204 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5 / Num. unique all: 1533 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHARPphasing
Cootmodel building
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→47.74 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.899 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23611 1568 5 %RANDOM
Rwork0.17402 ---
all0.18 31204 --
obs0.17713 29543 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.791 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5936 0 24 129 6089
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 124 -
Rwork0.18 2105 -
obs-31204 99.02 %

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