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- PDB-1kkr: CRYSTAL STRUCTURE OF CITROBACTER AMALONATICUS METHYLASPARTATE AMM... -

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Basic information

Entry
Database: PDB / ID: 1kkr
TitleCRYSTAL STRUCTURE OF CITROBACTER AMALONATICUS METHYLASPARTATE AMMONIA LYASE CONTAINING (2S,3S)-3-METHYLASPARTIC ACID
Components3-METHYLASPARTATE AMMONIA-LYASE
KeywordsLYASE / Methylaspartate ammonia lyase / Enolase superfamily / TIM barrel / substrate complex
Function / homology
Function and homology information


methylaspartate ammonia-lyase / methylaspartate ammonia-lyase activity / glutamate catabolic process via L-citramalate / metal ion binding
Similarity search - Function
Methylaspartate ammonia-lyase / Methylaspartate ammonia-lyase, C-terminal / Methylaspartate ammonia-lyase, N-terminal / Methylaspartate ammonia-lyase N-terminus / Methylaspartate ammonia-lyase C-terminus / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 ...Methylaspartate ammonia-lyase / Methylaspartate ammonia-lyase, C-terminal / Methylaspartate ammonia-lyase, N-terminal / Methylaspartate ammonia-lyase N-terminus / Methylaspartate ammonia-lyase C-terminus / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S,3S)-3-methyl-aspartic acid / Methylaspartate ammonia-lyase
Similarity search - Component
Biological speciesCitrobacter amalonaticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsLevy, C.W. / Buckley, P.A. / Sedelnikova, S. / Kato, K. / Asano, Y. / Rice, D.W. / Baker, P.J.
CitationJournal: Structure / Year: 2002
Title: Insights into enzyme evolution revealed by the structure of methylaspartate ammonia lyase.
Authors: Levy, C.W. / Buckley, P.A. / Sedelnikova, S. / Kato, Y. / Asano, Y. / Rice, D.W. / Baker, P.J.
History
DepositionDec 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 19, 2014Group: Derived calculations
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr3_auth_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_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

Downloads & links

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Assembly

Deposited unit
A: 3-METHYLASPARTATE AMMONIA-LYASE
B: 3-METHYLASPARTATE AMMONIA-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3236
Polymers91,9802
Non-polymers3434
Water11,331629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-42 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.537, 238.933, 66.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-808-

HOH

21B-552-

HOH

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Components

#1: Protein 3-METHYLASPARTATE AMMONIA-LYASE


Mass: 45989.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter amalonaticus (bacteria) / Gene: MAL / Plasmid: PMAL / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: O66145, methylaspartate ammonia-lyase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-2AS / (2S,3S)-3-methyl-aspartic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: potassium phosphate, ammonium sulphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Details: Levy, C.W., (2001) Acta Crystallogr., D57, 1922.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113 mg/mlprotein1drop
20.1 Mpotassium phosphate1reservoirpH8.0
332 %ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.1→18 Å / Num. all: 60480 / Num. obs: 60480 / Redundancy: 3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.2
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 5.1 / % possible all: 91.6
Reflection
*PLUS
Lowest resolution: 18 Å / % possible obs: 93.4 %
Reflection shell
*PLUS
% possible obs: 91.6 %

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementResolution: 2.1→18 Å / SU B: 5.805 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.176
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2858 5.1 %RANDOM
Rwork0.177 ---
obs0.179 53530 93.24 %-
Displacement parametersBiso mean: 25.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.24 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6291 0 22 629 6942
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it0.0450.847
X-RAY DIFFRACTIONp_mcangle_it21.576
X-RAY DIFFRACTIONp_scbond_it2.777
X-RAY DIFFRACTIONp_scangle_it4.069
LS refinement shellHighest resolution: 2.1 Å / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.184 / Total num. of bins used: 20
Refinement
*PLUS
Highest resolution: 2.1 Å / % reflection Rfree: 5.1 % / Rfactor obs: 0.167 / Rfactor Rfree: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.045
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it

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