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- PDB-2fgc: Crystal structure of Acetolactate synthase- small subunit from Th... -

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Basic information

Entry
Database: PDB / ID: 2fgc
TitleCrystal structure of Acetolactate synthase- small subunit from Thermotoga maritima
Componentsacetolactate synthase, small subunit
KeywordsTRANSFERASE / ACETOLACTATE SYNTHASE / REGULATORY SUBUNIT / STRUCTURAL GENOMICS / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


acetolactate synthase regulator activity / acetolactate synthase / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / cytosol
Similarity search - Function
Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / AHAS-like ACT domain / ACT-like. Chain A, domain 2 / Acetolactate synthase/Transcription factor NikR, C-terminal / ACT domain / ACT domain / ACT domain profile. ...Acetolactate synthase, small subunit, C-terminal / Small subunit of acetolactate synthase / Acetolactate synthase, small subunit / AHAS, ACT domain / AHAS-like ACT domain / ACT-like. Chain A, domain 2 / Acetolactate synthase/Transcription factor NikR, C-terminal / ACT domain / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Acetolactate synthase small subunit
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPetkowski, J.J. / Chruszcz, M. / Zimmerman, M.D. / Zheng, H. / Cymborowski, M.T. / Koclega, K.D. / Kudritska, M. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2007
Title: Crystal structures of TM0549 and NE1324--two orthologs of E. coli AHAS isozyme III small regulatory subunit.
Authors: Petkowski, J.J. / Chruszcz, M. / Zimmerman, M.D. / Zheng, H. / Skarina, T. / Onopriyenko, O. / Cymborowski, M.T. / Koclega, K.D. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionDec 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 24, 2012Group: Database references
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: acetolactate synthase, small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3932
Polymers22,3691
Non-polymers241
Water73941
1
A: acetolactate synthase, small subunit
hetero molecules

A: acetolactate synthase, small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7864
Polymers44,7372
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4530 Å2
ΔGint-40 kcal/mol
Surface area16040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.782, 104.782, 78.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein acetolactate synthase, small subunit


Mass: 22368.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: pET15b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS
References: GenBank: 4981064, UniProt: Q9WZ19*PLUS, acetolactate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2% V/V GLYCEROL, 0.4% W/V NDSB201, 0.15M MG FORMATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 19, 2005 / Details: SI 111 CHANNEL
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→27.26 Å / Num. all: 9510 / Num. obs: 9510 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 35.89
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
Cootmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→27.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.695 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23643 479 4.8 %RANDOM
Rwork0.168 ---
obs0.17663 9497 99.94 %-
all-9497 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.906 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 0 1 41 1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221250
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.9691689
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0515160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.9222450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.75915232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7331510
X-RAY DIFFRACTIONr_chiral_restr0.130.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02906
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.2469
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.2860
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4950.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2473818
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.18651299
X-RAY DIFFRACTIONr_scbond_it11.3658466
X-RAY DIFFRACTIONr_scangle_it16.03411390
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 35 -
Rwork0.174 683 -
obs--100 %

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