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- PDB-5yum: Crystallographic structures of IlvN.Val/Ile complexes:Conformatio... -

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Basic information

Entry
Database: PDB / ID: 5yum
TitleCrystallographic structures of IlvN.Val/Ile complexes:Conformational selectivity for feedback inhibition of AHASs
ComponentsAcetolactate synthase isozyme 1 small subunit
KeywordsTRANSFERASE / Transferase subunit / Regulatory subunit / ACT protein / amino acid binding
Function / homology
Function and homology information


acetolactate synthase regulator activity / acetolactate synthase complex / acetolactate synthase / branched-chain amino acid biosynthetic process / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / cytosol
Similarity search - Function
Acetolactate synthase, small subunit / AHAS, ACT domain / : / AHAS small subunit-like ACT domain / ACT domain / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / Alpha-Beta Plaits ...Acetolactate synthase, small subunit / AHAS, ACT domain / : / AHAS small subunit-like ACT domain / ACT domain / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / ISOLEUCINE / Acetolactate synthase isozyme 1 small subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.432 Å
AuthorsSarma, S.P. / Bansal, A. / Schindelin, H. / Demeler, B.
Funding support India, 1items
OrganizationGrant numberCountry
DSTO1544 India
Citation
Journal: Biochemistry / Year: 2019
Title: Crystallographic Structures of IlvN·Val/Ile Complexes: Conformational Selectivity for Feedback Inhibition of Aceto Hydroxy Acid Synthases.
Authors: Bansal, A. / Karanth, N.M. / Demeler, B. / Schindelin, H. / Sarma, S.P.
#1: Journal: Biochemistry / Year: 2013
Title: The coil-to-helix transition in IlvN regulates the allosteric control of Escherichia coli acetohydroxyacid synthase I.
Authors: Karanth, N.M. / Sarma, S.P.
#2: Journal: Biochemistry / Year: 2008
Title: Escherichia coli ilvN interacts with the FAD binding domain of ilvB and activates the AHAS I enzyme.
Authors: Mitra, A. / Sarma, S.P.
History
DepositionNov 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetolactate synthase isozyme 1 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4533
Polymers11,2631
Non-polymers1902
Water46826
1
A: Acetolactate synthase isozyme 1 small subunit
hetero molecules

A: Acetolactate synthase isozyme 1 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9066
Polymers22,5262
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area2500 Å2
ΔGint-19 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.620, 89.620, 86.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-102-

CO

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Components

#1: Protein Acetolactate synthase isozyme 1 small subunit / Acetohydroxy-acid synthase I small subunit / ALS-I


Mass: 11262.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ilvN, b3670, JW3645 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADF8, acetolactate synthase
#2: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 288 K / Method: microbatch / pH: 6.5
Details: 0.01M cobalt(II) chloride hexahydrate, 0.1M MES monohydrate pH 6.5, 1.8M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.43→57.88 Å / Num. obs: 5202 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.031 / Rrim(I) all: 0.075 / Net I/σ(I): 20.7
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 534 / CC1/2: 0.949 / Rpim(I) all: 0.195 / Rrim(I) all: 0.037 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXv1.13-2998-000refinement
iMOSFLMv7.0data reduction
Aimlessv7.0data scaling
PHASERv7.0phasing
REFMACv7.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LVW

2lvw


Resolution: 2.432→57.878 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.69
RfactorNum. reflection% reflection
Rfree0.2261 353 6.81 %
Rwork0.191 --
obs0.1936 5187 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.432→57.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms727 0 10 26 763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003752
X-RAY DIFFRACTIONf_angle_d0.6211022
X-RAY DIFFRACTIONf_dihedral_angle_d7.981631
X-RAY DIFFRACTIONf_chiral_restr0.046120
X-RAY DIFFRACTIONf_plane_restr0.004135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4323-2.78430.29311170.21451580X-RAY DIFFRACTION100
2.7843-3.50780.26211040.20691614X-RAY DIFFRACTION100
3.5078-57.89430.19951320.17671640X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -3.862 Å / Origin y: 22.5038 Å / Origin z: 1.109 Å
111213212223313233
T0.249 Å2-0.0019 Å20.006 Å2-0.2831 Å2-0.0013 Å2--0.3432 Å2
L5.4458 °2-0.7097 °2-0.1742 °2-6.4943 °2-0.1352 °2--6.2998 °2
S-0.2885 Å °-0.2545 Å °0.128 Å °-0.2611 Å °0.0401 Å °-0.5522 Å °-0.3746 Å °0.5986 Å °0.1933 Å °
Refinement TLS groupSelection details: all

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