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- PDB-3hv1: Crystal structure of a polar amino acid ABC uptake transporter su... -

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Basic information

Entry
Database: PDB / ID: 3hv1
TitleCrystal structure of a polar amino acid ABC uptake transporter substrate binding protein from Streptococcus thermophilus
ComponentsPolar amino acid ABC uptake transporter substrate binding protein
KeywordsTRANSPORT PROTEIN / Polar amino acid / ABC uptake transporter / Protein Structure Initiative II(PSI II) / NYSGXRC / 11316l / Structural Genomics / New York SGX Research Center for Structural Genomics
Function / homologyBacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta / Polar amino acid ABC uptake transporter substrate binding protein
Function and homology information
Biological speciesStreptococcus thermophilus LMG 18311 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsPalani, K. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a polar amino acid ABC uptake transporter substrate binding protein from Streptococcus thermophilus
Authors: Palani, K. / Burley, S.K. / Swaminathan, S.
History
DepositionJun 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: 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 / 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 1.3Nov 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

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Assembly

Deposited unit
A: Polar amino acid ABC uptake transporter substrate binding protein
B: Polar amino acid ABC uptake transporter substrate binding protein


Theoretical massNumber of molelcules
Total (without water)61,0102
Polymers61,0102
Non-polymers00
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Polar amino acid ABC uptake transporter substrate binding protein


Theoretical massNumber of molelcules
Total (without water)30,5051
Polymers30,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Polar amino acid ABC uptake transporter substrate binding protein


Theoretical massNumber of molelcules
Total (without water)30,5051
Polymers30,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.559, 78.563, 80.030
Angle α, β, γ (deg.)90.00, 105.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polar amino acid ABC uptake transporter substrate binding protein / ABC uptake transporter


Mass: 30505.230 Da / Num. of mol.: 2 / Fragment: residues 27-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus LMG 18311 (bacteria)
Gene: stu0877 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5M4P7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M L-Proline, 0.1M HEPES, 10% Polyethylene glycol monomethyl ether 2000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2009 / Details: MIRRORS
RadiationMonochromator: Si(III) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→45.02 Å / Num. all: 44250 / Num. obs: 44250 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 19.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4333 / % possible all: 97.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→45.02 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 248640.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2133 5 %RANDOM
Rwork0.222 ---
obs0.222 42840 95.6 %-
all-44250 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.0617 Å2 / ksol: 0.353258 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-6.07 Å20 Å2-0.47 Å2
2---1.55 Å20 Å2
3----4.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 0 281 4391
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 340 5.1 %
Rwork0.28 6273 -
obs-4333 89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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