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- PDB-3woa: Crystal structure of lambda repressor (1-45) fused with maltose-b... -

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Basic information

Entry
Database: PDB / ID: 3woa
TitleCrystal structure of lambda repressor (1-45) fused with maltose-binding protein
ComponentsRepressor protein CI, Maltose-binding periplasmic protein
KeywordsDNA BINDING PROTEIN / SUGAR BINDING PROTEIN / LAMBDA REPRESSOR / MALTOSE-BINDING PROTEIN
Function / homology
Function and homology information


maintenance of viral latency / latency-replication decision / positive regulation of viral transcription / negative regulation of transcription by competitive promoter binding / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport ...maintenance of viral latency / latency-replication decision / positive regulation of viral transcription / negative regulation of transcription by competitive promoter binding / 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 / core promoter sequence-specific DNA binding / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / identical protein binding / membrane
Similarity search - Function
LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / 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
Similarity search - Domain/homology
alpha-maltose / Repressor protein cI / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHanazono, Y. / Takeda, K. / Miki, K.
CitationJournal: FEBS Open Bio / Year: 2018
Title: Co-translational folding of alpha-helical proteins: structural studies of intermediate-length variants of the lambda repressor.
Authors: Hanazono, Y. / Takeda, K. / Miki, K.
History
DepositionDec 25, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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

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Assembly

Deposited unit
A: Repressor protein CI, Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2582
Polymers45,9161
Non-polymers3421
Water8,989499
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.865, 52.622, 58.271
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

21A-635-

HOH

31A-667-

HOH

41A-678-

HOH

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Components

#1: Protein Repressor protein CI, Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 45916.035 Da / Num. of mol.: 1 / Mutation: N416R
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL RESIDUES 0-45 FROM REPRESSOR PROTEIN CI (P03034) FUSED WITH MALTOSE-BINDING PERIPLASMIC PROTEIN (P0AEX9)
Source: (gene. exp.) Enterobacteria phage lambda (virus), (gene. exp.) Escherichia coli (E. coli)
Strain: K12 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P03034, UniProt: P0AEX9
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.6M DL-Malic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32189 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rsym value: 0.126 / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 11.3 / Rsym value: 0.179 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF

1anf


Resolution: 2→34.682 Å / FOM work R set: 0.8805 / SU ML: 0.15 / σ(F): 1.35 / Phase error: 18.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1939 1632 5.08 %random
Rwork0.1581 ---
obs0.1599 32126 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.7 Å2 / Biso mean: 18.17 Å2 / Biso min: 4.46 Å2
Refinement stepCycle: LAST / Resolution: 2→34.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 23 499 3727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093300
X-RAY DIFFRACTIONf_angle_d1.124468
X-RAY DIFFRACTIONf_dihedral_angle_d12.9861233
X-RAY DIFFRACTIONf_chiral_restr0.074488
X-RAY DIFFRACTIONf_plane_restr0.005576
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0004-2.05920.23561260.160224902616
2.0592-2.12570.21271490.160424822631
2.1257-2.20160.2161410.155124722613
2.2016-2.28980.2051430.151325232666
2.2898-2.39390.21311420.157824972639
2.3939-2.52010.18781440.166224982642
2.5201-2.6780.22121140.169925312645
2.678-2.88460.20711390.177325492688
2.8846-3.17470.20831310.172625362667
3.1747-3.63370.16841250.149425882713
3.6337-4.57640.15381470.135725862733
4.5764-34.68680.18651310.161727422873

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