[English] 日本語
Yorodumi
- PDB-5ypp: Crystal structure of IlvN.Val-1a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ypp
TitleCrystal structure of IlvN.Val-1a
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
ACETATE ION / DI(HYDROXYETHYL)ETHER / VALINE / Acetolactate synthase isozyme 1 small subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 2, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,29422
Polymers67,5776
Non-polymers1,71716
Water2,414134
1
A: Acetolactate synthase isozyme 1 small subunit
B: Acetolactate synthase isozyme 1 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0787
Polymers22,5262
Non-polymers5535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-14 kcal/mol
Surface area9010 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)23,0787
Polymers22,5262
Non-polymers5535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-11 kcal/mol
Surface area9110 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)23,1378
Polymers22,5262
Non-polymers6126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-12 kcal/mol
Surface area9270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.030, 80.620, 66.040
Angle α, β, γ (deg.)90.00, 119.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10:17 or resid 19 or (resid...
21(chain B and (resid 10:17 or resid 19 or (resid...
31(chain C and (resid 10:17 or resid 19 or (resid...
41(chain D and (resid 10:17 or resid 19 or (resid...
51(chain E and (resid 10:17 or resid 19 or (resid...
61(chain F and (resid 10:17 or resid 19 or (resid...

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
11ASNASNVALVAL(chain A and (resid 10:17 or resid 19 or (resid...AA10 - 1710 - 17
12ASNASNASNASN(chain A and (resid 10:17 or resid 19 or (resid...AA1919
13HISHISHISHIS(chain A and (resid 10:17 or resid 19 or (resid...AA2020
14ASPASPGLNGLN(chain A and (resid 10:17 or resid 19 or (resid...AA9 - 989 - 98
15ASPASPGLNGLN(chain A and (resid 10:17 or resid 19 or (resid...AA9 - 989 - 98
16ASPASPGLNGLN(chain A and (resid 10:17 or resid 19 or (resid...AA9 - 989 - 98
17ASPASPGLNGLN(chain A and (resid 10:17 or resid 19 or (resid...AA9 - 989 - 98
18ASPASPGLNGLN(chain A and (resid 10:17 or resid 19 or (resid...AA9 - 989 - 98
21ASNASNVALVAL(chain B and (resid 10:17 or resid 19 or (resid...BB10 - 1710 - 17
22ASNASNASNASN(chain B and (resid 10:17 or resid 19 or (resid...BB1919
23HISHISHISHIS(chain B and (resid 10:17 or resid 19 or (resid...BB2020
24ASPASPGLNGLN(chain B and (resid 10:17 or resid 19 or (resid...BB9 - 989 - 98
25ASPASPGLNGLN(chain B and (resid 10:17 or resid 19 or (resid...BB9 - 989 - 98
26ASPASPGLNGLN(chain B and (resid 10:17 or resid 19 or (resid...BB9 - 989 - 98
27ASPASPGLNGLN(chain B and (resid 10:17 or resid 19 or (resid...BB9 - 989 - 98
28ASPASPGLNGLN(chain B and (resid 10:17 or resid 19 or (resid...BB9 - 989 - 98
31ASNASNVALVAL(chain C and (resid 10:17 or resid 19 or (resid...CC10 - 1710 - 17
32ASNASNASNASN(chain C and (resid 10:17 or resid 19 or (resid...CC1919
33HISHISHISHIS(chain C and (resid 10:17 or resid 19 or (resid...CC2020
34ASPASPGLNGLN(chain C and (resid 10:17 or resid 19 or (resid...CC9 - 989 - 98
35ASPASPGLNGLN(chain C and (resid 10:17 or resid 19 or (resid...CC9 - 989 - 98
36ASPASPGLNGLN(chain C and (resid 10:17 or resid 19 or (resid...CC9 - 989 - 98
37ASPASPGLNGLN(chain C and (resid 10:17 or resid 19 or (resid...CC9 - 989 - 98
38ASPASPGLNGLN(chain C and (resid 10:17 or resid 19 or (resid...CC9 - 989 - 98
41ASNASNVALVAL(chain D and (resid 10:17 or resid 19 or (resid...DD10 - 1710 - 17
42ASNASNASNASN(chain D and (resid 10:17 or resid 19 or (resid...DD1919
43HISHISHISHIS(chain D and (resid 10:17 or resid 19 or (resid...DD2020
44ASPASPGLNGLN(chain D and (resid 10:17 or resid 19 or (resid...DD9 - 989 - 98
45ASPASPGLNGLN(chain D and (resid 10:17 or resid 19 or (resid...DD9 - 989 - 98
46ASPASPGLNGLN(chain D and (resid 10:17 or resid 19 or (resid...DD9 - 989 - 98
47ASPASPGLNGLN(chain D and (resid 10:17 or resid 19 or (resid...DD9 - 989 - 98
48ASPASPGLNGLN(chain D and (resid 10:17 or resid 19 or (resid...DD9 - 989 - 98
51ASNASNVALVAL(chain E and (resid 10:17 or resid 19 or (resid...EE10 - 1710 - 17
52ASNASNASNASN(chain E and (resid 10:17 or resid 19 or (resid...EE1919
53HISHISHISHIS(chain E and (resid 10:17 or resid 19 or (resid...EE2020
54HISHISGLNGLN(chain E and (resid 10:17 or resid 19 or (resid...EE8 - 988 - 98
55HISHISGLNGLN(chain E and (resid 10:17 or resid 19 or (resid...EE8 - 988 - 98
56HISHISGLNGLN(chain E and (resid 10:17 or resid 19 or (resid...EE8 - 988 - 98
57HISHISGLNGLN(chain E and (resid 10:17 or resid 19 or (resid...EE8 - 988 - 98
58HISHISGLNGLN(chain E and (resid 10:17 or resid 19 or (resid...EE8 - 988 - 98
61ASNASNVALVAL(chain F and (resid 10:17 or resid 19 or (resid...FF10 - 1710 - 17
62ASNASNASNASN(chain F and (resid 10:17 or resid 19 or (resid...FF1919
63HISHISHISHIS(chain F and (resid 10:17 or resid 19 or (resid...FF2020
64ASPASPGLNGLN(chain F and (resid 10:17 or resid 19 or (resid...FF9 - 989 - 98
65ASPASPGLNGLN(chain F and (resid 10:17 or resid 19 or (resid...FF9 - 989 - 98
66ASPASPGLNGLN(chain F and (resid 10:17 or resid 19 or (resid...FF9 - 989 - 98
67ASPASPGLNGLN(chain F and (resid 10:17 or resid 19 or (resid...FF9 - 989 - 98
68ASPASPGLNGLN(chain F and (resid 10:17 or resid 19 or (resid...FF9 - 989 - 98

-
Components

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


Mass: 11262.869 Da / Num. of mol.: 6
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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ADF8, acetolactate synthase
#2: Chemical
ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.4 %
Description: The crystals were flat and platy. The protein crystallised in a monoclinic crystal system with P21 as the point group.
Crystal growTemperature: 288 K / Method: microbatch / pH: 8.5
Details: 0.2M Sodium acetate trihydrate, 0.1M Tris HCl, pH 8.5, 30% PEG 4000

-
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
Reflection twinOperator: h,-k,-h-l / Fraction: 0.33
ReflectionResolution: 1.9→57.2 Å / Num. obs: 47251 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.039 / Rrim(I) all: 0.057 / Net I/σ(I): 15.1
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3094 / CC1/2: 0.672 / Rpim(I) all: 0.402 / Rrim(I) all: 0.601 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXv1.13-2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LVW

2lvw


Resolution: 1.9→33.022 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.8 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1703 2052 4.34 %
Rwork0.1484 --
obs0.1503 47227 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→33.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4351 0 115 134 4600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034607
X-RAY DIFFRACTIONf_angle_d0.5656218
X-RAY DIFFRACTIONf_dihedral_angle_d14.3242803
X-RAY DIFFRACTIONf_chiral_restr0.046717
X-RAY DIFFRACTIONf_plane_restr0.003812
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1882X-RAY DIFFRACTION9.661TORSIONAL
12B1882X-RAY DIFFRACTION9.661TORSIONAL
13C1882X-RAY DIFFRACTION9.661TORSIONAL
14D1882X-RAY DIFFRACTION9.661TORSIONAL
15E1882X-RAY DIFFRACTION9.661TORSIONAL
16F1882X-RAY DIFFRACTION9.661TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9035-1.94770.2358990.26242998X-RAY DIFFRACTION97
1.9477-1.99630.27821230.23753017X-RAY DIFFRACTION96
1.9963-2.05010.2711410.22012936X-RAY DIFFRACTION95
2.0501-2.11020.21661410.22132950X-RAY DIFFRACTION95
2.1102-2.1780.23711230.20423015X-RAY DIFFRACTION96
2.178-2.25550.23921330.19792966X-RAY DIFFRACTION96
2.2555-2.34540.20341280.20252998X-RAY DIFFRACTION96
2.3454-2.45160.24321740.19212980X-RAY DIFFRACTION94
2.4516-2.580.20131380.1762933X-RAY DIFFRACTION96
2.58-2.74040.21131020.16913082X-RAY DIFFRACTION97
2.7404-2.95010.2081990.16672980X-RAY DIFFRACTION97
2.9501-3.24340.15981680.15712973X-RAY DIFFRACTION95
3.2434-3.70450.18141410.13733017X-RAY DIFFRACTION96
3.7045-4.63670.1181740.09632944X-RAY DIFFRACTION94
4.6367-13.66150.13481680.09943008X-RAY DIFFRACTION93
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)
14.48551.6324-0.40624.9373-0.29873.4549-0.13040.1041-0.3172-0.12640.05790.03930.38980.13050.07640.20570.01750.04610.2138-0.02560.206618.318132.76549.9875
25.5187-0.4231-1.67693.46610.34733.57880.10350.25870.5604-0.119-0.00580.1304-0.3568-0.0626-0.08190.2213-0.02150.03910.17390.01520.246715.863748.58138.1468
34.8044-0.23771.58584.615-1.20693.86590.19330.0359-0.7447-0.0431-0.0693-0.14710.531-0.1183-0.06380.2273-0.0445-0.03580.2198-0.01510.3073-12.755932.824622.4334
44.28510.86331.4353.25330.37114.64-0.0155-0.27140.34940.1873-0.14810.0245-0.4471-0.18220.14520.2204-0.0058-0.03010.2186-0.00330.2124-12.709948.720125.1906
53.90910.3268-0.49964.4408-0.52296.50180.15730.03690.1822-0.1802-0.1095-0.2366-0.16210.3089-0.02850.22490.01380.01260.1539-0.00610.155716.131948.316241.8312
63.1638-0.7083-0.69944.51911.29264.73920.11330.0348-0.524-0.0261-0.08110.00920.8917-0.0724-0.03390.43380.0081-0.04360.20930.02580.221513.222332.534743.0531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 9:101)
2X-RAY DIFFRACTION2(chain B and resseq 9:101)
3X-RAY DIFFRACTION3(chain C and resseq 9:101)
4X-RAY DIFFRACTION4(chain D and resseq 9:101)
5X-RAY DIFFRACTION5(chain F and resseq 9:101)
6X-RAY DIFFRACTION6(chain E and resseq 8:101)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more