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- PDB-3r6q: A triclinic-lattice structure of aspartase from Bacillus sp. YM55-1 -

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Basic information

Entry
Database: PDB / ID: 3r6q
TitleA triclinic-lattice structure of aspartase from Bacillus sp. YM55-1
ComponentsAspartaseAspartate ammonia-lyase
KeywordsLYASE / aspartase / aspartate ammonia lyase
Function / homology
Function and homology information


aspartate ammonia-lyase / aspartate ammonia-lyase activity / aspartate metabolic process / tricarboxylic acid cycle / metal ion binding
Similarity search - Function
Aspartate ammonia-lyase / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 ...Aspartate ammonia-lyase / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Aspartate ammonia-lyase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFibriansah, G. / Puthan Veetil, V. / Poelarends, G.J. / Thunnissen, A.-M.W.H.
CitationJournal: Biochemistry / Year: 2011
Title: Structural basis for the catalytic mechanism of aspartate ammonia lyase.
Authors: Fibriansah, G. / Veetil, V.P. / Poelarends, G.J. / Thunnissen, A.M.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_dist_value / _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_label_asym_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: Aspartase
B: Aspartase
C: Aspartase
D: Aspartase
E: Aspartase
F: Aspartase
G: Aspartase
H: Aspartase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,72012
Polymers413,5608
Non-polymers1604
Water15,997888
1
A: Aspartase
B: Aspartase
C: Aspartase
D: Aspartase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,8606
Polymers206,7804
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29880 Å2
ΔGint-163 kcal/mol
Surface area57250 Å2
MethodPISA
2
E: Aspartase
F: Aspartase
G: Aspartase
H: Aspartase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,8606
Polymers206,7804
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29960 Å2
ΔGint-156 kcal/mol
Surface area57660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.594, 118.194, 140.226
Angle α, β, γ (deg.)89.850, 89.590, 76.510
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Aspartase / Aspartate ammonia-lyase


Mass: 51694.977 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: YM55-1 / Gene: aspB / Plasmid: pBAD/Myc-His A / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q9LCC6, aspartate ammonia-lyase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 888 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.25 M NaSCN, 10 mM CaCl2, 0.1 M HEPES, pH 7.0, 20% PEG3350, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 25, 2009
RadiationMonochromator: Diamond (111)and Ge (220) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.4→140.222 Å / Num. all: 161833 / Num. obs: 161833 / % possible obs: 87.6 % / Redundancy: 1.7 % / Rsym value: 0.058 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.531.70.2463.140425243260.24689.9
2.53-2.681.70.1874.138329229210.18789.8
2.68-2.871.70.1345.836076213770.13489.2
2.87-3.11.70.1037.533566197270.10388.4
3.1-3.391.70.06911.230955180300.06987.8
3.39-3.791.70.04317.428023161200.04386.7
3.79-4.381.80.03122.424783140910.03186.2
4.38-5.371.80.0272420927116960.02784.5
5.37-7.591.80.02823.21612288500.02883.1
7.59-48.2341.90.0222.6871046950.0280.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J3U

1j3u


Resolution: 2.4→39.56 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.88 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 16.865 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 8118 5 %RANDOM
Rwork0.1987 ---
obs0.2014 161826 87.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.94 Å2 / Biso mean: 27.4008 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.12 Å2-0.18 Å2
2--0.2 Å2-0.16 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28552 0 4 888 29444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02229041
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.96639301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.09653709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.59925.5381291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.625155213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.45415128
X-RAY DIFFRACTIONr_chiral_restr0.0840.24515
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02121700
X-RAY DIFFRACTIONr_mcbond_it0.4441.518382
X-RAY DIFFRACTIONr_mcangle_it0.854229705
X-RAY DIFFRACTIONr_scbond_it1.378310659
X-RAY DIFFRACTIONr_scangle_it2.2984.59595
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 617 -
Rwork0.252 11681 -
all-12298 -
obs--89.94 %
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)
10.26120.01960.04720.10430.01820.23540.0410.0123-0.01170.0073-0.029-0.00420.05550.0058-0.0120.0170.0026-0.00760.0096-0.00170.03470.0040.2530.034
20.26350.0321-0.06090.0939-0.02330.22610.04250.01170.00460.0083-0.03050.0051-0.0559-0.0083-0.01190.01690.00320.00170.01240.00020.031837.58450.141-70.153
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 466
2X-RAY DIFFRACTION1B5 - 466
3X-RAY DIFFRACTION1C5 - 466
4X-RAY DIFFRACTION1D5 - 466
5X-RAY DIFFRACTION2E5 - 466
6X-RAY DIFFRACTION2F4 - 466
7X-RAY DIFFRACTION2G5 - 466
8X-RAY DIFFRACTION2H5 - 466

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