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

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Basic information

Entry
Database: PDB / ID: 3zvh
TitleMethylaspartate ammonia lyase from Clostridium tetanomorphum mutant Q73A
Components(METHYLASPARTATE AMMONIA- ...) x 2
KeywordsLYASE / ENOLASE
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 / MOLECULAR REPLACEMENT / Resolution: 1.99 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
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)97,47510
Polymers96,9312
Non-polymers5458
Water9,584532
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-53.7 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.788, 109.705, 110.096
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, 0.004411, -0.006059), (0.004989, 0.9951, -0.09895), (0.005592, -0.09898, -0.9951)
Vector: -53.2173, -1.92835, -40.2901)

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Components

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METHYLASPARTATE AMMONIA- ... , 2 types, 2 molecules AB

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


Mass: 48449.262 Da / Num. of mol.: 1 / 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
#2: Protein METHYLASPARTATE AMMONIA-LYASE / 3-METHYLASPARTATE AMMONIA LYASE / BETA-METHYLASPARTASE


Mass: 48481.262 Da / Num. of mol.: 1 / 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 , 4 types, 540 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 532 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 73 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLN 73 TO ALA

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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 10, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→38.9 Å / Num. obs: 54091 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / % possible all: 95.4

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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: 1.99→77.71 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.875 / SU B: 7.887 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24889 2785 5 %RANDOM
Rwork0.19495 ---
obs0.19768 52449 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.506 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.52 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.99→77.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 33 532 6969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226563
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9688846
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7224.996843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15424.564298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.864151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.061546
X-RAY DIFFRACTIONr_chiral_restr0.0920.2986
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214918
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_it0.4711.54122
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80826616
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4532441
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1884.52230
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: 1.993→2.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 190 -
Rwork0.151 3389 -
obs--87.42 %
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)
10.2352-0.1718-0.0680.12650.04890.0355-0.01490.0092-0.04130.01260.00560.0295-0.018-0.01170.00940.06690.0043-0.00990.0878-0.00940.0254-38.9590.803-29.173
20.12780.0603-0.01730.73350.16260.0854-0.00630.0108-0.0206-0.0292-0.00080.0081-0.01140.00170.00710.0628-0.0009-0.00380.0707-0.00450.01-41.2328.271-30.286
30.56660.11440.21340.2608-0.00340.4561-0.0698-0.02930.0207-0.00360.04710.0476-0.0503-0.01630.02260.06650.0036-0.00120.0719-0.00170.0121-42.7219.041-17.654
41.15640.0152-0.13820.3683-0.25140.4284-0.0034-0.0916-0.17580.00560.02320.03810.00180.0188-0.01980.05010.00430.00630.07430.0340.0379-37.251-11.645-3.547
51.19360.33980.13451.3456-0.48820.4059-0.0028-0.084-0.01410.02320.0180.0642-0.0271-0.0547-0.01520.03520.01420.0140.10940.03070.0182-54.203-2.119-4.509
60.4508-0.0008-0.01830.0558-0.02780.1105-0.0415-0.05010.01120.02220.03270.0159-0.0130.00580.00880.07890.0140.00540.08120.00490.0088-36.0679.961-11.179
70.47920.033-0.09810.0039-0.00830.0224-0.0195-0.0592-0.08650.0086-0.0036-0.0075-0.00310.01640.0230.07140.00720.00090.09120.01080.0266-13.4610.133-9.684
80.3957-0.58050.06381.3182-0.020.1459-0.0269-0.06190.02640.02070.0322-0.102-0.00460.0256-0.00530.060.0003-0.00090.08180.00820.0107-11.05914.427-11.572
90.64770.481-0.17470.4125-0.10481.52360.0144-0.0259-0.01520.05640.0005-0.0635-0.11430.0467-0.01490.07590.0012-0.02640.0898-0.00980.0629-3.78917.67-17.812
100.29150.12520.08770.23840.14170.2043-0.00610.04290.0331-0.0035-0.0108-0.021-0.02350.03220.0170.0783-0.0098-0.0010.09680.00640.0185-16.2116.92-31.249
110.488-0.0169-0.07130.22890.01290.13690.00430.0481-0.03860.0173-0.0047-0.01890.0140.01580.00040.06760.0074-0.00440.0806-0.02050.0087-9.563-10.441-35.898
120.3474-0.0854-0.01690.2181-0.03790.12240.00360.0671-0.00040.00690.00120.0133-0.01860.0084-0.00480.0734-0.00920.00080.0779-0.01060.0054-16.5488.953-30.32
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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