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- PDB-4n03: Fatty acid ABC transporter substrate-binding protein from Thermom... -

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Basic information

Entry
Database: PDB / ID: 4n03
TitleFatty acid ABC transporter substrate-binding protein from Thermomonospora curvata
ComponentsABC-type branched-chain amino acid transport systems periplasmic component-like protein
KeywordsTRANSPORT PROTEIN / structural genomics / fatty acid / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / ABC-type branched-chain amino acid transport systems periplasmic component-like protein
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsOsipiuk, J. / Li, H. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Fatty acid ABC transporter substrate-binding protein from Thermomonospora curvata
Authors: Osipiuk, J. / Li, H. / Endres, M. / Joachimiak, A.
History
DepositionSep 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC-type branched-chain amino acid transport systems periplasmic component-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6623
Polymers43,3441
Non-polymers3182
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.409, 40.303, 72.557
Angle α, β, γ (deg.)90.000, 90.600, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asymmetric unit

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Components

#1: Protein ABC-type branched-chain amino acid transport systems periplasmic component-like protein


Mass: 43343.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (bacteria) / Strain: DSM 43183 / Gene: NC_013510.1:3663026..3664297, Tcur_3166 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D1A9M1
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris buffer, 2.5 M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.15→35.2 Å / Num. all: 123840 / Num. obs: 123840 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.081 / Χ2: 2.156 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.15-1.172.70.4072.2443100.74166.5
1.17-1.192.90.38452060.80380
1.19-1.213.30.35659530.93292
1.21-1.243.70.33361520.86694.9
1.24-1.273.80.29561990.92395.4
1.27-1.33.80.26262561.00895.8
1.3-1.333.80.23161751.06896
1.33-1.363.80.20462891.20896.4
1.36-1.43.80.17762721.32696.6
1.4-1.453.80.16163511.61396.9
1.45-1.53.80.13862921.93597.1
1.5-1.567.50.20863481.45597.7
1.56-1.637.60.16863911.70497.8
1.63-1.727.60.14863951.98298.1
1.72-1.837.60.12664362.26598.5
1.83-1.977.60.10764592.46898.7
1.97-2.167.50.09464792.58199.1
2.16-2.487.40.08265432.80199.4
2.48-3.127.30.07265863.83399.5
3.12-506.70.06167484.47799.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.15→35.2 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / Occupancy max: 1 / Occupancy min: 0.26 / SU B: 1.285 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1493 6264 5.1 %RANDOM
Rwork0.1237 ---
all0.125 123819 --
obs0.125 123819 94.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.68 Å2 / Biso mean: 16.8082 Å2 / Biso min: 8.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-2.12 Å2
2---1.01 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.15→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 0 22 467 3410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023371
X-RAY DIFFRACTIONr_bond_other_d0.0010.023398
X-RAY DIFFRACTIONr_angle_refined_deg1.6952.0034630
X-RAY DIFFRACTIONr_angle_other_deg0.8493.0017953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7075493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68525.588136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36515616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5151513
X-RAY DIFFRACTIONr_chiral_restr0.1030.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213894
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02699
X-RAY DIFFRACTIONr_rigid_bond_restr11.90836769
X-RAY DIFFRACTIONr_sphericity_free25.626595
X-RAY DIFFRACTIONr_sphericity_bonded8.89757029
LS refinement shellResolution: 1.149→1.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 327 -
Rwork0.236 6286 -
all-6613 -
obs-6603 68.51 %

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