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

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Basic information

Entry
Database: PDB / ID: 3ble
TitleCrystal structure of the catalytic domain of LiCMS in complexed with malonate
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
MALONATE ION / (R)-citramalate synthase CimA
Similarity search - Component
Biological speciesLeptospira interrogans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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.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_ref_seq_dif.details / _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
A: Citramalate synthase from Leptospira interrogans
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7733
Polymers37,6061
Non-polymers1672
Water2,774154
1
A: Citramalate synthase from Leptospira interrogans
hetero molecules

A: Citramalate synthase from Leptospira interrogans
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5466
Polymers75,2112
Non-polymers3354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5520 Å2
ΔGint-79.7 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.158, 85.158, 112.897
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-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.14 Å3/Da / Density % sol: 60.86 % / Mosaicity: 0.391 °
Crystal growTemperature: 293 K / pH: 7.5
Details: 0.1M HEPES, 2.0M Sodium malonate, pH7.5, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 21.8 % / Av σ(I) over netI: 13.4 / Number: 332159 / Rmerge(I) obs: 0.081 / Χ2: 1.17 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 15263 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.65099.910.061.86319.9
4.455.610010.0441.07921.5
3.884.4510010.0491.01721.8
3.533.8810010.0651.05922
3.283.5310010.0931.11322
3.083.2810010.1331.1222.1
2.933.0810010.1831.1422.1
2.82.9310010.2611.13322.2
2.692.810010.3261.11722.2
2.62.6910010.4311.12322.2
ReflectionResolution: 1.85→50 Å / Num. obs: 41014 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.068 / Χ2: 0.975 / Net I/σ(I): 10.2
Reflection shellResolution: 1.99→2.08 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.427 / Num. unique all: 4051 / Χ2: 0.993 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementResolution: 2→39.84 Å / σ(F): 731
RfactorNum. reflection% reflection
Rfree0.254 1573 4.8 %
Rwork0.223 --
obs-31828 97.7 %
Solvent computationBsol: 63.786 Å2
Displacement parametersBiso mean: 39.444 Å2
Baniso -1Baniso -2Baniso -3
1-4.858 Å21.797 Å20 Å2
2--4.858 Å20 Å2
3----9.715 Å2
Refinement stepCycle: LAST / Resolution: 2→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 8 154 2586
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4mli.param

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