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- PDB-3bli: Crystal structure of the catalytic domain of LiCMS in complexed w... -

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Basic information

Entry
Database: PDB / ID: 3bli
TitleCrystal structure of the catalytic domain of LiCMS in complexed with pyruvate and acetyl-CoA
ComponentsCitramalate synthase from Leptospira interrogans
KeywordsTRANSFERASE / TIM barrel / LiCMSN / substrate specificity / Acyltransferase / Amino-acid biosynthesis / Branched-chain amino acid biosynthesis / Leucine biosynthesis
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
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. / Aldolase class I ...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. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / PYRUVIC ACID / (R)-citramalate synthase CimA
Similarity search - Component
Biological speciesLeptospira interrogans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsZhang, P. / Ma, J.
CitationJournal: Biochem.J. / Year: 2008
Title: Molecular basis of the substrate specificity and the catalytic mechanism of citramalate synthase from Leptospira interrogans
Authors: Ma, J. / Zhang, P. / Zhang, Z. / Zha, M. / Xu, H. / Zhao, G. / Ding, J.
History
DepositionDec 11, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Citramalate synthase from Leptospira interrogans
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5694
Polymers37,6061
Non-polymers9633
Water1,47782
1
A: Citramalate synthase from Leptospira interrogans
hetero molecules

A: Citramalate synthase from Leptospira interrogans
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1378
Polymers75,2112
Non-polymers1,9266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area8090 Å2
ΔGint-90.5 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.990, 84.990, 115.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Citramalate synthase from Leptospira interrogans


Mass: 37605.523 Da / Num. of mol.: 1 / Fragment: UNP residues 1-325
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, 2-isopropylmalate synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES, 2.0M Sodium malonate, pH7.5, vapor diffusion, temperature 293K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→19.95 Å / Num. all: 17171 / Num. obs: 16591 / % possible obs: 96.6 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.104

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BLE

3ble


Resolution: 2.5→19.29 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.281 831 4.8 %
Rwork0.229 --
obs-16561 96.4 %
Solvent computationBsol: 53.691 Å2
Displacement parametersBiso mean: 43.534 Å2
Baniso -1Baniso -2Baniso -3
1-5.24 Å2-1.838 Å20 Å2
2--5.24 Å20 Å2
3----10.479 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 58 82 2587
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3pyr.param
X-RAY DIFFRACTION4water.param
X-RAY DIFFRACTION5aco.param

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