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- PDB-3f6g: Crystal structure of the regulatory domain of LiCMS in complexed ... -

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Basic information

Entry
Database: PDB / ID: 3f6g
TitleCrystal structure of the regulatory domain of LiCMS in complexed with isoleucine - type II
ComponentsAlpha-isopropylmalate synthase
KeywordsTRANSFERASE / LiCMSC / allosteric regulation / feedback inhibition / selectivity / specificity / Acyltransferase
Function / homology
Function and homology information


(R)-citramalate synthase / (R)-citramalate synthase activity / 2-isopropylmalate synthase activity / L-leucine biosynthetic process / isoleucine biosynthetic process / lyase activity / metal ion binding
Similarity search - Function
Double Stranded RNA Binding Domain - #340 / Double Stranded RNA Binding Domain - #740 / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain superfamily / LeuA allosteric (dimerisation) domain / LeuA allosteric (dimerisation) domain / Alpha-isopropylmalate and homocitrate synthases signature 1. / Alpha-isopropylmalate/homocitrate synthase, conserved site / Pyruvate carboxyltransferase / HMGL-like ...Double Stranded RNA Binding Domain - #340 / Double Stranded RNA Binding Domain - #740 / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain / 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain superfamily / LeuA allosteric (dimerisation) domain / LeuA allosteric (dimerisation) domain / Alpha-isopropylmalate and homocitrate synthases signature 1. / Alpha-isopropylmalate/homocitrate synthase, conserved site / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Double Stranded RNA Binding Domain / Aldolase-type TIM barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOLEUCINE / (R)-citramalate synthase CimA
Similarity search - Component
Biological speciesLeptospira interrogans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZhang, P. / Ma, J. / Zhao, G. / Ding, J.
CitationJournal: Biochem.J. / Year: 2009
Title: Molecular basis of the inhibitor selectivity and insights into the feedback inhibition mechanism of citramalate synthase from Leptospira interrogans
Authors: Zhang, P. / Ma, J. / Zhang, Z. / Zha, M. / Xu, H. / Zhao, G. / Ding, J.
History
DepositionNov 6, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Alpha-isopropylmalate synthase
A: Alpha-isopropylmalate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,63814
Polymers28,4772
Non-polymers1,16212
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-123.8 kcal/mol
Surface area10750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.315, 97.943, 39.974
Angle α, β, γ (deg.)90.000, 91.380, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-358-

ZN

21A-359-

ZN

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Components

#1: Protein Alpha-isopropylmalate synthase / Citramalate synthase


Mass: 14238.300 Da / Num. of mol.: 2 / Fragment: Regulatory domain, UNP residues 390-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans (bacteria) / Strain: 56601 / Gene: cimA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8F3Q1, EC: 2.3.1.182
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ILE / ISOLEUCINE / Isoleucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, pH8.0, 1.6M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONPhoton Factory BL-6A20.9789, 0.9796, 0.9643
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEMar 24, 2007
ADSC QUANTUM 42CCDMar 3, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97891
30.97961
40.96431
ReflectionResolution: 2→20 Å / Num. obs: 15916 / Redundancy: 3.8 % / Rmerge(I) obs: 0.076
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.327 / Num. unique all: 5456

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.263 794 5.1 %RANDOM
Rwork0.226 ---
obs0.227 15562 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 90.46 Å2 / Biso mean: 33.646 Å2 / Biso min: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å2-0.01 Å2
2---1.77 Å20 Å2
3---3.87 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 60 167 2054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211907
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9742574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6935232
X-RAY DIFFRACTIONr_chiral_restr0.0990.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021360
X-RAY DIFFRACTIONr_nbd_refined0.2870.21001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2124
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3480.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.212
X-RAY DIFFRACTIONr_mcbond_it1.4411.51178
X-RAY DIFFRACTIONr_mcangle_it2.52321904
X-RAY DIFFRACTIONr_scbond_it2.2783729
X-RAY DIFFRACTIONr_scangle_it3.3994.5670
X-RAY DIFFRACTIONr_rigid_bond_restr2.38121907
X-RAY DIFFRACTIONr_sphericity_free02169
X-RAY DIFFRACTIONr_sphericity_bonded021887
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.323 49
Rwork0.332 1077
all-1126

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