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- PDB-1hsj: SARR MBP FUSION STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1hsj
TitleSARR MBP FUSION STRUCTURE
ComponentsFUSION PROTEIN CONSISTING OF STAPHYLOCOCCUS ACCESSORY REGULATOR PROTEIN R AND MALTOSE BINDING PROTEIN
KeywordsTranscription/Sugar Binding Protein / Novel fold for DNA binding / Transcription-Sugar Binding Protein COMPLEX
Function / homology
Function and homology information


response to stress / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...response to stress / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA-binding transcription factor activity / DNA damage response / DNA binding / membrane / cytoplasm
Similarity search - Function
Transcriptional regulator SarA/Rot / : / Transcriptional regulator SarA/Rot / : / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II ...Transcriptional regulator SarA/Rot / : / Transcriptional regulator SarA/Rot / : / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein / HTH-type transcriptional regulator SarR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of the SarR protein from Staphylococcus aureus.
Authors: Liu, Y. / Manna, A. / Li, R. / Martin, W.E. / Murphy, R.C. / Cheung, A.L. / Zhang, G.
History
DepositionDec 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _struct_ref.db_code / _struct_ref.db_name ..._struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.ndb_seq_num
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FUSION PROTEIN CONSISTING OF STAPHYLOCOCCUS ACCESSORY REGULATOR PROTEIN R AND MALTOSE BINDING PROTEIN
B: FUSION PROTEIN CONSISTING OF STAPHYLOCOCCUS ACCESSORY REGULATOR PROTEIN R AND MALTOSE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5766
Polymers108,8562
Non-polymers7214
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-5 kcal/mol
Surface area41050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.739, 70.639, 75.473
Angle α, β, γ (deg.)65.72, 67.18, 69.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein FUSION PROTEIN CONSISTING OF STAPHYLOCOCCUS ACCESSORY REGULATOR PROTEIN R AND MALTOSE BINDING PROTEIN / SARR AND MBP / MMBP


Mass: 54427.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Staphylococcus aureus (bacteria)
Genus: Escherichia, Staphylococcus / Species: , / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEY0, UniProt: Q2YYV0, UniProt: P0AEX9*PLUS
#2: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
25 mMbeta-mercaptoethanol1reservoir
3100 mMsodium acetate1reservoir
4100 mM1reservoirNaCl
518-22 %PEGmme20001reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99
DetectorDetector: CCD / Date: Nov 12, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.28→40 Å / Num. all: 50256 / Num. obs: 50256 / % possible obs: 89.9 % / Redundancy: 2 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.028 / Rsym value: 0.032 / Net I/σ(I): 25.1
Reflection shellResolution: 2.28→2.37 Å / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.3 / % possible all: 84.8
Reflection
*PLUS
Num. obs: 37403 / % possible obs: 96.5 % / Num. measured all: 77545

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Maltose binding protein 4mbp

4mbp


Resolution: 2.3→19.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 381018.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.304 1962 5 %RANDOM
Rwork0.263 ---
obs0.263 39144 80.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.14 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso mean: 71.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å21.88 Å2-2.13 Å2
2--9.4 Å2-4.01 Å2
3----9.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7684 0 48 0 7732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.431 199 5 %
Rwork0.404 3803 -
obs--49.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAM
X-RAY DIFFRACTION3WATER.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 37186 / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.2324 / Rfactor Rfree: 0.2822
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 71.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Lowest resolution: 2.4 Å / Rfactor Rfree: 0.3802 / % reflection Rfree: 5 % / Rfactor Rwork: 0.404 / Num. reflection Rwork: 2702 / Rfactor obs: 0.4156

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