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- PDB-1kd0: Crystal Structure of beta-methylaspartase from Clostridium tetano... -

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Basic information

Entry
Database: PDB / ID: 1kd0
TitleCrystal Structure of beta-methylaspartase from Clostridium tetanomorphum. Apo-structure.
Componentsbeta-methylaspartase
KeywordsLYASE / beta zigzag / alpha/beta-barrel
Function / homology
Function and homology information


methylaspartate ammonia-lyase / methylaspartate ammonia-lyase activity / L-glutamate catabolic process via L-citramalate / cobalamin binding / 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
Methylaspartate ammonia-lyase
Similarity search - Component
Biological speciesClostridium tetanomorphum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsAsuncion, M. / Blankenfeldt, W. / Barlow, J.N. / Gani, D. / Naismith, J.H.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: The structure of 3-methylaspartase from Clostridium tetanomorphum functions via the common enolase chemical step.
Authors: Asuncion, M. / Blankenfeldt, W. / Barlow, J.N. / Gani, D. / Naismith, J.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Overexpression, purification, crystallization and data collection of 3-methylaspartase from Clostridium tetanomorphum
Authors: Asuncion, M. / Barlow, J.N. / Pollard, J. / Staines, A.G. / McMahon, S.A. / Blankenfeldt, W. / Gani, D. / Naismith, J.H.
History
DepositionNov 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / software / 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.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: beta-methylaspartase
B: beta-methylaspartase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9034
Polymers92,7792
Non-polymers1242
Water11,872659
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-20 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.281, 109.260, 108.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homodimer.

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Components

#1: Protein beta-methylaspartase / METHYLASPARTATE AMMONIA-LYASE


Mass: 46389.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Plasmid: pGetita / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q05514, methylaspartate ammonia-lyase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Tris-HCl, NaCl, PEG6000, ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-25 %(w/v)PEG60001reservoir
2100 mMsodium acetate1reservoirpH7.0
325 mMTris-HCl1reservoirpH7.0
416-22 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.946439 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946439 Å / Relative weight: 1
ReflectionResolution: 1.9→30.86 Å / Num. all: 64042 / Num. obs: 63750 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.9 / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.1
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 0.019 / % possible all: 99.9
Reflection
*PLUS
Redundancy: 3.9 % / Num. measured all: 249409
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
SnBphasing
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→57.74 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.2 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.15 / Stereochemistry target values: Engh & Huber
Details: TLS-option in REFMAC5 with 3 TLS groups for protein chains and water molecules. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3228 5 %RANDOM
Rwork0.175 ---
all0.178 60746 --
obs0.178 60746 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Solvent model: BABINET model with mask parameters for mask calculation
Displacement parametersBiso mean: 33.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.148 Å0.161 Å
Refinement stepCycle: LAST / Resolution: 1.9→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6374 0 8 659 7041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0226582
X-RAY DIFFRACTIONr_bond_other_d0.0010.026071
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.9598924
X-RAY DIFFRACTIONr_angle_other_deg0.976314126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8373868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.966151229
X-RAY DIFFRACTIONr_chiral_restr0.1370.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027430
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021288
X-RAY DIFFRACTIONr_nbd_refined0.2380.31539
X-RAY DIFFRACTIONr_nbd_other0.2090.36110
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.5603
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0890.510
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.336
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5460.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1841.54144
X-RAY DIFFRACTIONr_mcangle_it1.98426708
X-RAY DIFFRACTIONr_scbond_it3.63632438
X-RAY DIFFRACTIONr_scangle_it5.2664.52216
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 227 -
Rwork0.251 --
obs-4709 99.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.47170.0924-0.02650.30260.14870.18930.0117-0.07150.09740.0049-0.00910.0563-0.0346-0.1485-0.00270.0335-0.00480.00070.08020.01530.02339.06512.72724.344
20.7744-0.0419-0.19450.2592-0.04830.499-0.0492-0.1329-0.0506-0.02280.0246-0.0170.01920.0610.02470.0268-0.01060.00240.02280.01090.014438.354-0.05924.344
30.50240.174-0.17110.22040.05880.4233-0.0127-0.0937-0.1390.01450.0228-0.13040.14060.1099-0.01010.0875-0.03470.00290.02060.00030.038825.6664.65924.335
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 413
2X-RAY DIFFRACTION2B1 - 413
3X-RAY DIFFRACTION3A702 - 1016
4X-RAY DIFFRACTION3B703 - 1046
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.031
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.052
LS refinement shell
*PLUS
Rfactor Rfree: 0.29 / Rfactor obs: 0.251

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