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- PDB-5ypw: Crystal structure of IlvN.Val-1b -

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Basic information

Entry
Database: PDB / ID: 5ypw
TitleCrystal structure of IlvN.Val-1b
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 / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process
Similarity search - Function
Acetolactate synthase, small subunit / AHAS, ACT domain / ACT domain / ACT domain / ACT domain profile. / ACT domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
VALINE / Acetolactate synthase isozyme 1 small subunit
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 3, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetolactate synthase isozyme 1 small subunit
B: Acetolactate synthase isozyme 1 small subunit
C: Acetolactate synthase isozyme 1 small subunit
D: Acetolactate synthase isozyme 1 small subunit
E: Acetolactate synthase isozyme 1 small subunit
F: Acetolactate synthase isozyme 1 small subunit
G: Acetolactate synthase isozyme 1 small subunit
H: Acetolactate synthase isozyme 1 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,04016
Polymers90,1038
Non-polymers9378
Water1,49583
1
A: Acetolactate synthase isozyme 1 small subunit
B: Acetolactate synthase isozyme 1 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7604
Polymers22,5262
Non-polymers2342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-20 kcal/mol
Surface area8710 Å2
MethodPISA
2
C: Acetolactate synthase isozyme 1 small subunit
D: Acetolactate synthase isozyme 1 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7604
Polymers22,5262
Non-polymers2342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-22 kcal/mol
Surface area8570 Å2
MethodPISA
3
E: Acetolactate synthase isozyme 1 small subunit
F: Acetolactate synthase isozyme 1 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7604
Polymers22,5262
Non-polymers2342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-20 kcal/mol
Surface area9060 Å2
MethodPISA
4
G: Acetolactate synthase isozyme 1 small subunit
H: Acetolactate synthase isozyme 1 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7604
Polymers22,5262
Non-polymers2342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-19 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.040, 74.670, 88.810
Angle α, β, γ (deg.)90.00, 99.37, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 9 and (name N or name...
21(chain B and ((resid 9 and (name N or name...
31(chain C and (resid 9 through 19 or (resid 20...
41(chain D and (resid 9 through 19 or (resid 20...
51(chain E and ((resid 9 and (name N or name...
61(chain F and (resid 9 through 19 or (resid 20...
71(chain G and (resid 9 through 19 or (resid 20...
81(chain H and ((resid 9 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASPASP(chain A and ((resid 9 and (name N or name...AA99
12ASPASPGLNGLN(chain A and ((resid 9 and (name N or name...AA9 - 989 - 98
13ASPASPGLNGLN(chain A and ((resid 9 and (name N or name...AA9 - 989 - 98
14ASPASPGLNGLN(chain A and ((resid 9 and (name N or name...AA9 - 989 - 98
15ASPASPGLNGLN(chain A and ((resid 9 and (name N or name...AA9 - 989 - 98
21ASPASPASPASP(chain B and ((resid 9 and (name N or name...BB99
22ASPASPGLNGLN(chain B and ((resid 9 and (name N or name...BB9 - 989 - 98
23ASPASPGLNGLN(chain B and ((resid 9 and (name N or name...BB9 - 989 - 98
24ASPASPGLNGLN(chain B and ((resid 9 and (name N or name...BB9 - 989 - 98
25ASPASPGLNGLN(chain B and ((resid 9 and (name N or name...BB9 - 989 - 98
31ASPASPASNASN(chain C and (resid 9 through 19 or (resid 20...CC9 - 199 - 19
32HISHISHISHIS(chain C and (resid 9 through 19 or (resid 20...CC2020
33ASPASPGLNGLN(chain C and (resid 9 through 19 or (resid 20...CC9 - 989 - 98
34ASPASPGLNGLN(chain C and (resid 9 through 19 or (resid 20...CC9 - 989 - 98
35ASPASPGLNGLN(chain C and (resid 9 through 19 or (resid 20...CC9 - 989 - 98
36ASPASPGLNGLN(chain C and (resid 9 through 19 or (resid 20...CC9 - 989 - 98
41ASPASPASNASN(chain D and (resid 9 through 19 or (resid 20...DD9 - 199 - 19
42HISHISHISHIS(chain D and (resid 9 through 19 or (resid 20...DD2020
43ASPASPGLNGLN(chain D and (resid 9 through 19 or (resid 20...DD9 - 989 - 98
44ASPASPGLNGLN(chain D and (resid 9 through 19 or (resid 20...DD9 - 989 - 98
45ASPASPGLNGLN(chain D and (resid 9 through 19 or (resid 20...DD9 - 989 - 98
51ASPASPASPASP(chain E and ((resid 9 and (name N or name...EE99
52ASPASPGLNGLN(chain E and ((resid 9 and (name N or name...EE9 - 989 - 98
53ASPASPGLNGLN(chain E and ((resid 9 and (name N or name...EE9 - 989 - 98
54ASPASPGLNGLN(chain E and ((resid 9 and (name N or name...EE9 - 989 - 98
55ASPASPGLNGLN(chain E and ((resid 9 and (name N or name...EE9 - 989 - 98
61ASPASPASNASN(chain F and (resid 9 through 19 or (resid 20...FF9 - 199 - 19
62HISHISHISHIS(chain F and (resid 9 through 19 or (resid 20...FF2020
63HISHISGLNGLN(chain F and (resid 9 through 19 or (resid 20...FF8 - 988 - 98
71ASPASPASNASN(chain G and (resid 9 through 19 or (resid 20...GG9 - 199 - 19
72HISHISHISHIS(chain G and (resid 9 through 19 or (resid 20...GG2020
73ASPASPGLNGLN(chain G and (resid 9 through 19 or (resid 20...GG9 - 989 - 98
81ASPASPASPASP(chain H and ((resid 9 and (name N or name...HH99
82ASPASPGLNGLN(chain H and ((resid 9 and (name N or name...HH9 - 989 - 98
83ASPASPGLNGLN(chain H and ((resid 9 and (name N or name...HH9 - 989 - 98
84ASPASPGLNGLN(chain H and ((resid 9 and (name N or name...HH9 - 989 - 98
85ASPASPGLNGLN(chain H and ((resid 9 and (name N or name...HH9 - 989 - 98

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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.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ilvN, Z5164, ECs4611 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ADG0, acetolactate synthase
#2: Chemical
ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 288 K / Method: microbatch / pH: 5.6
Details: 0.2M ammonium acetate, 0.1M Sodium citrate tribasic dihydrate, pH5.6, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→62.2 Å / Num. obs: 36346 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 30 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.114 / Net I/σ(I): 5.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.635 / Num. unique obs: 3568 / CC1/2: 0.775 / Rpim(I) all: 0.6 / Rrim(I) all: 0.876 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(v1.13_2998)refinement
iMOSFLM7.2.1data reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LVW

2lvw


Resolution: 2.3→47.791 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.34
RfactorNum. reflection% reflection
Rfree0.2334 1769 4.87 %
Rwork0.1829 --
obs0.1853 36297 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5669 0 64 83 5816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085830
X-RAY DIFFRACTIONf_angle_d1.17908
X-RAY DIFFRACTIONf_dihedral_angle_d9.3043709
X-RAY DIFFRACTIONf_chiral_restr0.066945
X-RAY DIFFRACTIONf_plane_restr0.0081028
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A0X-RAY DIFFRACTION0TORSIONAL
12B0X-RAY DIFFRACTION0TORSIONAL
13C0X-RAY DIFFRACTION0TORSIONAL
14D0X-RAY DIFFRACTION0TORSIONAL
15E0X-RAY DIFFRACTION0TORSIONAL
16F0X-RAY DIFFRACTION0TORSIONAL
17G0X-RAY DIFFRACTION0TORSIONAL
18H0X-RAY DIFFRACTION0TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.36230.34021560.26082629X-RAY DIFFRACTION100
2.3623-2.43180.29931170.24422675X-RAY DIFFRACTION100
2.4318-2.51030.31881190.23962661X-RAY DIFFRACTION100
2.5103-2.60.26411230.22242625X-RAY DIFFRACTION100
2.6-2.70410.2621360.21052659X-RAY DIFFRACTION100
2.7041-2.82710.29861310.2252636X-RAY DIFFRACTION100
2.8271-2.97610.27491540.21232647X-RAY DIFFRACTION100
2.9761-3.16260.26261300.19582642X-RAY DIFFRACTION100
3.1626-3.40670.2331430.18752649X-RAY DIFFRACTION100
3.4067-3.74940.21811400.16492655X-RAY DIFFRACTION100
3.7494-4.29160.21481270.15532663X-RAY DIFFRACTION100
4.2916-5.40580.17721420.14222669X-RAY DIFFRACTION100
5.4058-47.80090.18651510.15852718X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8112-0.7931-1.30734.695-0.71552.49460.1764-0.12350.6002-0.0010.05810.668-0.2596-0.2664-0.1570.1921-0.00750.0270.1465-0.01410.4561-27.085420.7063-39.4519
24.5284-0.50990.21593.1998-0.68593.35430.0806-0.477-0.2364-0.0026-0.1363-0.12650.14490.12530.0680.1569-0.02410.01610.18290.01120.4695-16.35618.1977-37.5853
35.20880.7279-0.91494.6152.00394.56420.0244-0.10250.93570.02920.066-0.1867-0.33160.0851-0.09770.1591-0.0244-0.00150.25-0.05730.618913.30813.9804-32.5486
45.0918-0.0736-1.1464.2926-0.48544.7822-0.2566-0.0905-0.59650.26020.34090.44170.4229-0.1645-0.02280.24490.0145-0.00380.2209-0.00870.66875.6075-9.7539-30.2808
52.51560.1437-0.48735.0620.05482.6943-0.00990.13290.0011-0.14150.0231-0.2035-0.15360.0764-0.0060.1216-0.0055-0.0120.12930.00420.3509-23.585622.8434-5.8216
63.82820.00781.21993.89260.14783.3693-0.05920.053-0.1078-0.0030.05250.22430.1743-0.330.01520.1357-0.0253-0.00110.0820.0140.2508-34.141110.0479-5.165
75.17110.21721.40844.30542.36045.0325-0.00030.3406-0.33320.08960.1199-0.15810.34990.3644-0.10960.16360.03950.0120.2549-0.01520.56436.00926.558-10.748
85.12950.28960.48783.80060.40094.7836-0.20160.40360.6909-0.39690.24810.3252-0.5379-0.0816-0.01230.2817-0.0414-0.05060.25140.03710.7333-1.611940.5372-13.6509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 9:98)
2X-RAY DIFFRACTION2(chain B and resseq 9:98)
3X-RAY DIFFRACTION3(chain C and resseq 10:98)
4X-RAY DIFFRACTION4(chain D and resseq 10:98)
5X-RAY DIFFRACTION5(chain E and resseq 9:98)
6X-RAY DIFFRACTION6(chain F and resseq 9:98)
7X-RAY DIFFRACTION7(chain G and resseq 10:98)
8X-RAY DIFFRACTION8(chain H and resseq 9:98)

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