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- PDB-2f1f: Crystal structure of the regulatory subunit of acetohydroxyacid s... -

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Basic information

Entry
Database: PDB / ID: 2f1f
TitleCrystal structure of the regulatory subunit of acetohydroxyacid synthase isozyme III from E. coli
ComponentsAcetolactate synthase isozyme III small subunit
KeywordsTRANSFERASE / ferredoxin fold / ACT domain
Function / homology
Function and homology information


acetolactate synthase regulator activity / acetolactate synthase / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / cytosol
Similarity search - Function
ACT domain / Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / ACT-like. Chain A, domain 2 / Acetolactate synthase/Transcription factor NikR, C-terminal / ACT domain / ACT domain profile. / ACT domain ...ACT domain / Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / ACT-like. Chain A, domain 2 / Acetolactate synthase/Transcription factor NikR, C-terminal / ACT domain / ACT domain profile. / ACT domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetolactate synthase isozyme 3 small subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsKaplun, A. / Vyazmensky, M. / Barak, Z. / Chipman, D.M. / Shaanan, B.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of the Regulatory Subunit of Acetohydroxyacid Synthase Isozyme III from Escherichia coli.
Authors: Kaplun, A. / Vyazmensky, M. / Zherdev, Y. / Belenky, I. / Slutzker, A. / Mendel, S. / Barak, Z. / Chipman, D.M. / Shaanan, B.
History
DepositionNov 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AS A RESULT OF A CLONING ARTIFACT, AN ALANINE HAS BEEN INSERTED BETWEEN THE FIRST RESIDUE ...SEQUENCE AS A RESULT OF A CLONING ARTIFACT, AN ALANINE HAS BEEN INSERTED BETWEEN THE FIRST RESIDUE MET AND THE SECOND RESIDUE ARG. MET 1 IS NOT OBSERVED IN THE ELECTRON DENSITY, HENCE THE INSERTED ALA IS NUMBERED 1 IN THE ENTRY, WITH THE REST OF THE RESIDUES NUMBERED AS IN SWISSPROT ENTRY P00894.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetolactate synthase isozyme III small subunit
B: Acetolactate synthase isozyme III small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,85410
Polymers36,1442
Non-polymers7108
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-35 kcal/mol
Surface area14590 Å2
MethodPISA
2
A: Acetolactate synthase isozyme III small subunit
B: Acetolactate synthase isozyme III small subunit
hetero molecules

A: Acetolactate synthase isozyme III small subunit
B: Acetolactate synthase isozyme III small subunit
hetero molecules

A: Acetolactate synthase isozyme III small subunit
B: Acetolactate synthase isozyme III small subunit
hetero molecules

A: Acetolactate synthase isozyme III small subunit
B: Acetolactate synthase isozyme III small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,41740
Polymers144,5758
Non-polymers2,84232
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area30780 Å2
ΔGint-162 kcal/mol
Surface area48270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.600, 98.600, 80.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-801-

MG

21B-901-

MG

31B-805-

MG

41B-810-

MG

51A-803-

HOH

61A-804-

HOH

71A-878-

HOH

81A-896-

HOH

91B-903-

HOH

101B-904-

HOH

DetailsThe asymmetric unit contains the biological dimer

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Components

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


Mass: 18071.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ilvH, brnP / Plasmid: pUH / Production host: Escherichia coli (E. coli) / Strain (production host): XL-blue MRF' / References: UniProt: P00894, acetolactate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 10-25 mg/ml protein in 0.5 M MgCl2, 1:1 mixed with reservoir made up of 30-40% PEG400, 0.4-0.6 M MgCl2, 100 mM Tris-HCl pH 8.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97924, 0.97942, 0.93928
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 30, 2004 / Details: bent crystal
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1bent crystalMADMx-ray1
2bent crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.979421
30.939281
Reflection
IDAv σ(I) over netINumberRmerge(I) obsD res high (Å)Num. obs% possible obs
114.46196757725144599.5
215.451961576.625144899.5
316.031972446.225146499.5
ReflectionResolution: 1.75→40 Å / Num. all: 38313 / Num. obs: 38313 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.15 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.057 / Net I/σ(I): 15.1
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3076 / Num. unique obs: 2905 / Rsym value: 0.59 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_1240.270025161871
ISO_2240.270.8550.58925161871
ISO_3240.270.9110.58525161871
ANO_1240.271.470250540
ANO_2240.270.7820250890
ANO_3240.270.0630251020
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_18.75-40.270026044
ISO_16.26-8.750049647
ISO_15.13-6.260065043
ISO_14.45-5.130078543
ISO_13.99-4.450087948
ISO_13.64-3.990098545
ISO_13.38-3.6400106344
ISO_13.16-3.3800117546
ISO_12.98-3.1600121944
ISO_12.83-2.9800130946
ISO_12.7-2.8300134742
ISO_12.58-2.700146044
ISO_12.48-2.5800148638
ISO_12.39-2.4800155247
ISO_12.31-2.3900161140
ISO_12.24-2.3100169444
ISO_12.17-2.2400172240
ISO_12.11-2.1700178234
ISO_12.05-2.1100181147
ISO_12-2.0500187545
ANO_18.75-40.272.05302570
ANO_16.26-8.752.15604960
ANO_15.13-6.262.01306500
ANO_14.45-5.131.7107850
ANO_13.99-4.451.6108790
ANO_13.64-3.991.56209840
ANO_13.38-3.641.556010630
ANO_13.16-3.381.566011730
ANO_12.98-3.161.665012160
ANO_12.83-2.981.604013080
ANO_12.7-2.831.661013460
ANO_12.58-2.71.615014550
ANO_12.48-2.581.526014830
ANO_12.39-2.481.372015480
ANO_12.31-2.391.233016040
ANO_12.24-2.311.133016860
ANO_12.17-2.241.106017090
ANO_12.11-2.170.93017670
ANO_12.05-2.110.866017990
ANO_12-2.050.803018460
ISO_28.75-40.271.1090.57726044
ISO_26.26-8.751.5270.91849647
ISO_25.13-6.261.3590.98865043
ISO_24.45-5.131.0340.56778543
ISO_23.99-4.451.0250.68487948
ISO_23.64-3.991.050.69398545
ISO_23.38-3.641.0060.643106344
ISO_23.16-3.381.0530.602117546
ISO_22.98-3.161.0910.682121944
ISO_22.83-2.981.1010.81130946
ISO_22.7-2.831.0980.642134742
ISO_22.58-2.70.9840.543146044
ISO_22.48-2.580.9210.401148638
ISO_22.39-2.480.8080.401155247
ISO_22.31-2.390.7230.415161140
ISO_22.24-2.310.6240.365169444
ISO_22.17-2.240.5820.361172240
ISO_22.11-2.170.4820.217178234
ISO_22.05-2.110.4270.174181147
ISO_22-2.050.3760.147187545
ANO_28.75-40.271.50202580
ANO_26.26-8.751.58704960
ANO_25.13-6.261.34106490
ANO_24.45-5.131.15307850
ANO_23.99-4.451.02108790
ANO_23.64-3.990.98909850
ANO_23.38-3.640.873010630
ANO_23.16-3.380.977011730
ANO_22.98-3.160.943012170
ANO_22.83-2.980.965013080
ANO_22.7-2.830.879013450
ANO_22.58-2.70.845014560
ANO_22.48-2.580.768014830
ANO_22.39-2.480.675015480
ANO_22.31-2.390.622016060
ANO_22.24-2.310.542016880
ANO_22.17-2.240.507017100
ANO_22.11-2.170.428017690
ANO_22.05-2.110.388018000
ANO_22-2.050.36018710
ISO_38.75-40.270.8740.52726044
ISO_36.26-8.751.0130.77949647
ISO_35.13-6.261.0260.7665043
ISO_34.45-5.130.9820.56478543
ISO_33.99-4.450.9950.5687948
ISO_33.64-3.991.0560.6398545
ISO_33.38-3.640.9740.569106344
ISO_33.16-3.381.0050.54117546
ISO_32.98-3.161.0220.671121944
ISO_32.83-2.981.0170.726130946
ISO_32.7-2.831.0140.557134742
ISO_32.58-2.70.9830.508146044
ISO_32.48-2.580.9610.503148638
ISO_32.39-2.480.9040.489155247
ISO_32.31-2.390.8410.548161140
ISO_32.24-2.310.7790.386169444
ISO_32.17-2.240.7310.404172240
ISO_32.11-2.170.6510.257178234
ISO_32.05-2.110.5980.26181147
ISO_32-2.050.540.217187545
ANO_38.75-40.270.09702570
ANO_36.26-8.750.09104960
ANO_35.13-6.260.08806500
ANO_34.45-5.130.08307850
ANO_33.99-4.450.07508790
ANO_33.64-3.990.07309850
ANO_33.38-3.640.068010630
ANO_33.16-3.380.071011740
ANO_32.98-3.160.072012170
ANO_32.83-2.980.071013080
ANO_32.7-2.830.071013460
ANO_32.58-2.70.069014570
ANO_32.48-2.580.061014830
ANO_32.39-2.480.057015500
ANO_32.31-2.390.052016070
ANO_32.24-2.310.047016890
ANO_32.17-2.240.045017120
ANO_32.11-2.170.04017710
ANO_32.05-2.110.036018000
ANO_32-2.050.032018730
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
122.15921.6050SE45.260.57
221.84930.97328.107SE34.140.57
316.54114.77725.588SE16.70.49
437.73130.7524.806SE25.970.58
514.75330.17721.119SE33.020.64

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHARPphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.497 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1917 5 %RANDOM
Rwork0.171 ---
all0.174 38313 --
obs0.174 38302 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.821 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 52 258 2784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222534
X-RAY DIFFRACTIONr_angle_refined_deg2.1181.9983397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5165319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3123.396106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85615477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6081527
X-RAY DIFFRACTIONr_chiral_restr0.2430.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021801
X-RAY DIFFRACTIONr_nbd_refined0.2570.21209
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21715
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.229
X-RAY DIFFRACTIONr_mcbond_it2.61.51648
X-RAY DIFFRACTIONr_mcangle_it3.88322555
X-RAY DIFFRACTIONr_scbond_it5.5573973
X-RAY DIFFRACTIONr_scangle_it7.7054.5842
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 132 -
Rwork0.23 2654 -
obs-2786 100 %

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