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- PDB-6lu3: Crystal structure of a substrate binding protein from Microbacter... -

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Basic information

Entry
Database: PDB / ID: 6lu3
TitleCrystal structure of a substrate binding protein from Microbacterium hydrocarbonoxydans complexed with 4-hydroxybenzoate hydrazide
ComponentsSubstrate binding protein
KeywordsTRANSPORT PROTEIN / Complex
Function / homology4-oxidanylbenzohydrazide
Function and homology information
Biological speciesMicrobacterium hydrocarbonoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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 1.2Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7382
Polymers53,5861
Non-polymers1521
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18110 Å2
Unit cell
Length a, b, c (Å)51.296, 77.561, 121.711
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: 53585.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium hydrocarbonoxydans (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-HDH / 4-oxidanylbenzohydrazide / 4-hydroxybenzoic acid hydrazide


Mass: 152.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.26 Å3/Da / Density % sol: 45.55 %
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) PEG 8000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 25212 / % possible obs: 98.9 % / Redundancy: 5.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.203 / Net I/σ(I): 13.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1252 / CC1/2: 0.756 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→47.314 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.204
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2297 1297 5.153 %
Rwork0.2086 --
all0.21 --
obs-25168 98.048 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.864 Å2
Baniso -1Baniso -2Baniso -3
1--0.455 Å20 Å20 Å2
2--0.574 Å20 Å2
3----0.119 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 11 180 3728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133616
X-RAY DIFFRACTIONr_bond_other_d0.0370.0173258
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.6484946
X-RAY DIFFRACTIONr_angle_other_deg2.4121.5737545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.5495479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96723.029175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70715522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3371521
X-RAY DIFFRACTIONr_chiral_restr0.0710.2500
X-RAY DIFFRACTIONr_chiral_restr_other0.0560.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024185
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02740
X-RAY DIFFRACTIONr_nbd_refined0.1860.2645
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.23056
X-RAY DIFFRACTIONr_nbtor_refined0.1540.21780
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.21658
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2184
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0140.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3230.28
X-RAY DIFFRACTIONr_nbd_other0.3380.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1050.24
X-RAY DIFFRACTIONr_mcbond_it1.4713.061919
X-RAY DIFFRACTIONr_mcbond_other1.4713.0591918
X-RAY DIFFRACTIONr_mcangle_it2.3694.5852397
X-RAY DIFFRACTIONr_mcangle_other2.3684.5872398
X-RAY DIFFRACTIONr_scbond_it1.6993.2251697
X-RAY DIFFRACTIONr_scbond_other1.6983.2241698
X-RAY DIFFRACTIONr_scangle_it2.7724.7722549
X-RAY DIFFRACTIONr_scangle_other2.7724.7712550
X-RAY DIFFRACTIONr_lrange_it3.96235.4473856
X-RAY DIFFRACTIONr_lrange_other3.96235.4473856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2490.267820.2721536X-RAY DIFFRACTION85.9724
2.249-2.310.3371130.2721660X-RAY DIFFRACTION98.1184
2.31-2.3770.283970.2381624X-RAY DIFFRACTION98.1186
2.377-2.450.286920.2471629X-RAY DIFFRACTION98.3991
2.45-2.5310.239710.2391560X-RAY DIFFRACTION98.6094
2.531-2.6190.256720.2331503X-RAY DIFFRACTION98.6842
2.619-2.7180.25740.231485X-RAY DIFFRACTION98.9841
2.718-2.8290.238720.2181425X-RAY DIFFRACTION99.0735
2.829-2.9540.225640.2081362X-RAY DIFFRACTION99.0966
2.954-3.0980.239650.2191309X-RAY DIFFRACTION98.7779
3.098-3.2650.251720.2141242X-RAY DIFFRACTION99.3949
3.265-3.4630.236690.2161186X-RAY DIFFRACTION99.6032
3.463-3.7010.213740.1941115X-RAY DIFFRACTION99.3317
3.701-3.9970.177500.1731044X-RAY DIFFRACTION99.7265
3.997-4.3770.196680.167952X-RAY DIFFRACTION99.6094
4.377-4.890.138280.173906X-RAY DIFFRACTION99.6798
4.89-5.6420.229530.197779X-RAY DIFFRACTION100
5.642-6.8970.198350.217679X-RAY DIFFRACTION99.8601
6.897-9.70.226290.161543X-RAY DIFFRACTION99.6516
9.7-47.30.191170.209332X-RAY DIFFRACTION98.8669

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