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

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Basic information

Entry
Database: PDB / ID: 1kcz
TitleCrystal Structure of beta-methylaspartase from Clostridium tetanomorphum. Mg-complex.
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 1.3Mar 26, 2025Group: 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 / pdbx_struct_conn_angle / 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 / _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_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_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)91,4536
Polymers91,2802
Non-polymers1734
Water15,259847
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-37 kcal/mol
Surface area28840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.016, 108.783, 109.557
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: 45640.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Plasmid: pJGetita / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(lambda DE3)pLysS / References: UniProt: Q05514, 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 847 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Tris-HCl, NaCl, ethylene glycol, PEG 6000, 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: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 17, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→55.05 Å / Num. all: 63850 / Num. obs: 63452 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 4.3 / Redundancy: 11.4 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 9 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 4.3 / % possible all: 95.1
Reflection
*PLUS
Redundancy: 11.5 % / Num. measured all: 731140
Reflection shell
*PLUS
% possible obs: 95.1 %

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Processing

Software
NameVersionClassification
SnBphasing
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→76.7 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.782 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic temperature factors / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.118 / 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
Rfree0.17459 3210 5.1 %RANDOM
Rwork0.13498 ---
all0.13699 60342 --
obs0.13699 60342 99.53 %-
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 mean: 8.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2---1.29 Å20 Å2
3---1.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.118 Å0.127 Å
Refinement stepCycle: LAST / Resolution: 1.9→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6381 0 10 847 7238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0226543
X-RAY DIFFRACTIONr_bond_other_d0.0010.026033
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.968848
X-RAY DIFFRACTIONr_angle_other_deg0.827314033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5073848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.412151217
X-RAY DIFFRACTIONr_chiral_restr0.1140.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027352
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021278
X-RAY DIFFRACTIONr_nbd_refined0.2340.31492
X-RAY DIFFRACTIONr_nbd_other0.1990.36096
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.5709
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1490.56
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5520.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.336
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.480.533
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9721.54113
X-RAY DIFFRACTIONr_mcangle_it1.73426630
X-RAY DIFFRACTIONr_scbond_it3.09532430
X-RAY DIFFRACTIONr_scangle_it4.9384.52218
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
Rfree0.206 209 -
Rwork0.145 --
obs-4411 95.1 %
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)
10.26050.02770.03720.2680.02920.2435-0.00310.0461-0.0262-0.03250.011-0.09320.00950.0631-0.00790.04930.00390.01050.05290.00740.076441.1762.43114.294
20.57-0.0655-0.10470.465-0.03470.2699-0.0313-0.0152-0.08220.01810.00730.02780.0195-0.03190.0240.04920.00040.00070.0411-0.00540.049912.0312.47427.195
30.4428-0.0848-0.04990.29240.03780.2627-0.0081-0.0023-0.0438-0.0016-0.0169-0.00930.01130.00840.02490.0143-0.0046-0.00450.0025-0.00030.004825.8812.39921.065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 413
2X-RAY DIFFRACTION1A901
3X-RAY DIFFRACTION1A903
4X-RAY DIFFRACTION2B1 - 413
5X-RAY DIFFRACTION2B902
6X-RAY DIFFRACTION2B904
7X-RAY DIFFRACTION3A904 - 1302
8X-RAY DIFFRACTION3B905 - 1352
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 76.7 Å / σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.743
LS refinement shell
*PLUS
Rfactor Rfree: 0.206 / Rfactor Rwork: 0.145 / Rfactor obs: 0.145

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