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- PDB-6lu2: Crystal structure of a substrate binding protein from Microbacter... -

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Basic information

Entry
Database: PDB / ID: 6lu2
TitleCrystal structure of a substrate binding protein from Microbacterium hydrocarbonoxydans
ComponentsSubstrate binding protein
KeywordsTRANSPORT PROTEIN / Complex
Biological speciesMicrobacterium hydrocarbonoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsShimamura, K. / Akiyama, T. / Yokoyama, K. / Takenoya, M. / Ito, S. / Sasaki, Y. / Yajima, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K05398 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural basis of substrate recognition by the substrate binding protein (SBP) of a hydrazide transporter, obtained from Microbacterium hydrocarbonoxydans.
Authors: Shimamura, K. / Akiyama, T. / Yokoyama, K. / Takenoya, M. / Ito, S. / Sasaki, Y. / Yajima, S.
History
DepositionJan 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Substrate binding protein


Theoretical massNumber of molelcules
Total (without water)53,8671
Polymers53,8671
Non-polymers00
Water6,251347
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18870 Å2
Unit cell
Length a, b, c (Å)49.263, 78.443, 123.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Substrate binding protein


Mass: 53867.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium hydrocarbonoxydans (bacteria)
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS GAT74979 FOR THE PROTEIN.

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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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium acetate 0.1 M sodium cacodylate, pH 7.5 30% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9785 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 48691 / % possible obs: 99.3 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 50.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2301 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→39.551 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2064 2397 4.93 %
Rwork0.1941 --
all0.195 --
obs-48619 99.133 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.104 Å20 Å20 Å2
2--0.409 Å20 Å2
3----0.513 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 0 347 3893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133658
X-RAY DIFFRACTIONr_bond_other_d0.0370.0173289
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.6455011
X-RAY DIFFRACTIONr_angle_other_deg2.3941.5697629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.5185490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4523.146178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98315525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5411521
X-RAY DIFFRACTIONr_chiral_restr0.0620.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024262
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02745
X-RAY DIFFRACTIONr_nbd_refined0.1980.2702
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.23052
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21837
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.21596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0770.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1220.23
X-RAY DIFFRACTIONr_nbd_other0.1740.220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.212
X-RAY DIFFRACTIONr_mcbond_it1.6572.6021948
X-RAY DIFFRACTIONr_mcbond_other1.6572.6011947
X-RAY DIFFRACTIONr_mcangle_it2.4543.8982442
X-RAY DIFFRACTIONr_mcangle_other2.4543.92443
X-RAY DIFFRACTIONr_scbond_it2.3322.8121710
X-RAY DIFFRACTIONr_scbond_other2.3312.8141711
X-RAY DIFFRACTIONr_scangle_it3.5284.1282569
X-RAY DIFFRACTIONr_scangle_other3.5284.132570
X-RAY DIFFRACTIONr_lrange_it4.53532.0614058
X-RAY DIFFRACTIONr_lrange_other4.49831.9094004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.2651480.2833218X-RAY DIFFRACTION94.5506
1.795-1.8450.251870.2483249X-RAY DIFFRACTION98.9346
1.845-1.8980.2731630.2553221X-RAY DIFFRACTION99.0342
1.898-1.9560.2651540.2423109X-RAY DIFFRACTION99.2095
1.956-2.020.2471460.2173005X-RAY DIFFRACTION99.0881
2.02-2.0910.2571590.2222925X-RAY DIFFRACTION99.6768
2.091-2.170.2771630.2172819X-RAY DIFFRACTION99.5327
2.17-2.2590.2491320.2072761X-RAY DIFFRACTION99.6212
2.259-2.3590.2271390.1942612X-RAY DIFFRACTION99.7824
2.359-2.4740.2241260.1962532X-RAY DIFFRACTION99.8497
2.474-2.6080.2261150.1942412X-RAY DIFFRACTION100
2.608-2.7660.1881350.22255X-RAY DIFFRACTION99.9582
2.766-2.9560.2151040.2042160X-RAY DIFFRACTION100
2.956-3.1920.1951070.2012001X-RAY DIFFRACTION100
3.192-3.4960.1861020.1871881X-RAY DIFFRACTION100
3.496-3.9080.171920.1711671X-RAY DIFFRACTION100
3.908-4.510.168720.1531518X-RAY DIFFRACTION100
4.51-5.5170.169680.1511294X-RAY DIFFRACTION99.7802
5.517-7.7750.135520.1631018X-RAY DIFFRACTION99.8134
7.775-39.50.178330.192561X-RAY DIFFRACTION91.5254

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