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- PDB-3zvi: Methylaspartate ammonia lyase from Clostridium tetanomorphum muta... -

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Basic information

Entry
Database: PDB / ID: 3zvi
TitleMethylaspartate ammonia lyase from Clostridium tetanomorphum mutant L384A
ComponentsMETHYLASPARTATE AMMONIA-LYASE
KeywordsLYASE / ENOLASE
Function / homology
Function and homology information


methylaspartate ammonia-lyase / methylaspartate ammonia-lyase activity / L-glutamate fermentation 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
PROPIONAMIDE / Methylaspartate ammonia-lyase
Similarity search - Component
Biological speciesCLOSTRIDIUM TETANOMORPHUM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRaj, H. / Szymanski, W. / de Villiers, J. / Rozeboom, H.J. / Veetil, V.P. / Reis, C.R. / de Villiers, M. / de Wildeman, S. / Dekker, F.J. / Quax, W.J. ...Raj, H. / Szymanski, W. / de Villiers, J. / Rozeboom, H.J. / Veetil, V.P. / Reis, C.R. / de Villiers, M. / de Wildeman, S. / Dekker, F.J. / Quax, W.J. / Thunnissen, A.M.W.H. / Feringa, B.L. / Janssen, D.B. / Poelarends, G.J.
CitationJournal: Nat.Chem. / Year: 2012
Title: Engineering Methylaspartate Ammonia Lyase for the Asymmetric Synthesis of Unnatural Amino Acids.
Authors: Raj, H. / Szymanski, W. / De Villiers, J. / Rozeboom, H.J. / Veetil, V.P. / Reis, C.R. / De Villiers, M. / Dekker, F.J. / De Wildeman, S. / Quax, W.J. / Thunnissen, A.M.W.H. / Feringa, B.L. ...Authors: Raj, H. / Szymanski, W. / De Villiers, J. / Rozeboom, H.J. / Veetil, V.P. / Reis, C.R. / De Villiers, M. / Dekker, F.J. / De Wildeman, S. / Quax, W.J. / Thunnissen, A.M.W.H. / Feringa, B.L. / Janssen, D.B. / Poelarends, G.J.
History
DepositionJul 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,58712
Polymers96,8962
Non-polymers69110
Water14,340796
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-57.4 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.621, 109.863, 110.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.005002, -0.003176), (0.005336, 0.9933, -0.1157), (0.002576, -0.1157, -0.9933)
Vector: -52.9077, -2.21999, -40.1586)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein METHYLASPARTATE AMMONIA-LYASE / 3-METHYLASPARTATE AMMONIA LYASE / BETA-METHYLASPARTASE


Mass: 48448.238 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM TETANOMORPHUM (bacteria) / Strain: H1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: Q05514, methylaspartate ammonia-lyase

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Non-polymers , 5 types, 806 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ROP / PROPIONAMIDE


Mass: 73.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 796 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 384 TO ALA ENGINEERED RESIDUE IN CHAIN B, LEU 384 TO ALA
Has protein modificationY
Nonpolymer detailsPROPIONAMIDE (ROP): COVALENTLY ATTACHED TO CYS361

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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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 6 / Details: 14-17 % PEG6000, MES PH 6.0, 100 MM MGCL2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Nov 8, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→39 Å / Num. obs: 61377 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / % possible all: 87.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KCZ

1kcz


Resolution: 1.9→35.03 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.47 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20995 3103 5.1 %RANDOM
Rwork0.15999 ---
obs0.16252 58217 93.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.596 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2--1.82 Å20 Å2
3----2.88 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 43 796 7241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226571
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9688849
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.944.972841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57324.6300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.294151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8291546
X-RAY DIFFRACTIONr_chiral_restr0.0930.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214934
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5261.54126
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91226618
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.78532445
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8414.52231
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.896→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 212 -
Rwork0.224 3698 -
obs--82.39 %
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)
10.3791-0.0140.0810.98540.2150.07080.01-0.0009-0.0704-0.0219-0.0010.0741-0.0142-0.006-0.0090.0481-00.00010.0309-0.00090.0789-38.9050.712-29.376
20.2478-0.03610.03051.59270.25790.0518-0.0010.0202-0.017-0.063-0.02160.0831-0.0096-0.00990.02260.0450.0038-0.00870.0363-0.00260.0688-40.9867.941-30.26
30.59380.09580.16740.72020.03780.6027-0.0721-0.03390.05140.01240.04920.0714-0.0711-0.04880.02290.05010.023-0.0080.0289-0.00240.0528-42.35418.847-17.153
41.6687-0.0845-0.42840.7568-0.24990.9312-0.0204-0.025-0.1515-0.02120.01570.03050.07410.00080.00470.0383-0.0069-0.00710.01760.01050.0352-36.787-11.655-2.922
52.18360.0237-0.02041.95-0.77751.6835-0.0505-0.02780.0310.03240.07830.21510.0007-0.0355-0.02790.00620.0110.01560.06530.03010.0606-54.043-2.316-4.291
60.67620.0439-0.10560.4253-0.14180.3005-0.0212-0.06810.00780.05020.03390.0365-0.011-0.0285-0.01270.05620.0179-0.00380.04020.00290.0461-35.69910.066-11.024
70.60.162-0.12051.4855-0.46840.1974-0.0284-0.1069-0.0960.1182-0.0205-0.0728-0.03730.01410.04890.03980.0149-0.0160.04360.01450.0621-13.393-0.146-9.582
80.9322-1.1938-0.01692.8693-0.24860.4585-0.0568-0.01720.09270.0861-0.0054-0.1564-0.04720.07650.06220.03-0.023-0.02150.03320.0130.0684-10.74813.712-11.681
91.51620.98150.66922.0211-0.3782.20640.0287-0.14240.06580.0658-0.0467-0.1917-0.12330.12290.0180.0177-0.01440.0070.057-0.01350.1047-3.6917.325-18.058
100.18710.32970.0890.8770.06450.8296-0.02680.01580.0468-0.05-0.0185-0.02-0.08470.06650.04530.0285-0.0007-0.00130.02760.01130.0862-16.31816.495-31.375
111.34850.13050.09820.6977-0.08660.47880.03320.0962-0.07670.003-0.0271-0.02280.05290.0395-0.00610.03590.02-0.0010.0251-0.01350.0268-9.499-10.898-36.018
120.3881-0.0405-0.20420.07220.13390.33480.00920.0420.0323-0.01350.0051-0.0284-0.01010.0118-0.01420.0468-0.00130.00120.04290.01120.0768-16.5158.754-30.568
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 31
2X-RAY DIFFRACTION2A32 - 109
3X-RAY DIFFRACTION3A110 - 166
4X-RAY DIFFRACTION4A167 - 273
5X-RAY DIFFRACTION5A274 - 330
6X-RAY DIFFRACTION6A331 - 415
7X-RAY DIFFRACTION7B1 - 58
8X-RAY DIFFRACTION8B59 - 106
9X-RAY DIFFRACTION9B107 - 133
10X-RAY DIFFRACTION10B134 - 172
11X-RAY DIFFRACTION11B173 - 330
12X-RAY DIFFRACTION12B331 - 415

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