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- PDB-3r6y: Crystal structure of chymotrypsin-treated aspartase from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 3r6y
TitleCrystal structure of chymotrypsin-treated aspartase from Bacillus sp. YM55-1
ComponentsAspartase
KeywordsLYASE / aspartase / aspartate ammonia lyase
Function / homology
Function and homology information


aspartate ammonia-lyase / aspartate ammonia-lyase activity / aspartate metabolic process / tricarboxylic acid cycle / cytosol
Similarity search - Function
Aspartate ammonia-lyase / : / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) ...Aspartate ammonia-lyase / : / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / 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: 3 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_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_label_asym_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_label_asym_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_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

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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)354,30010
Polymers354,2208
Non-polymers802
Water1,08160
1
A: Aspartase
B: Aspartase
C: Aspartase
D: Aspartase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,1505
Polymers177,1104
Non-polymers401
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24550 Å2
ΔGint-97 kcal/mol
Surface area46310 Å2
MethodPISA
2
E: Aspartase
F: Aspartase
G: Aspartase
H: Aspartase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,1505
Polymers177,1104
Non-polymers401
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24640 Å2
ΔGint-96 kcal/mol
Surface area46470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.310, 168.940, 149.080
Angle α, β, γ (deg.)90.000, 92.230, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H
15G
25C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 310
2115E1 - 310
1215A330 - 400
2215E330 - 400
1125B1 - 310
2125F1 - 310
1225B330 - 400
2225F330 - 400
1135C1 - 310
2135G1 - 310
1235C330 - 400
2235G330 - 400
1145D1 - 310
2145H1 - 310
1245D330 - 400
2245H330 - 400
1152G315 - 317
2152C315 - 317

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein
Aspartase


Mass: 44277.473 Da / Num. of mol.: 8
Fragment: N-terminal and Central helix domains (UNP residues 1-401)
Source method: isolated from a genetically manipulated source
Details: After purification, the protein was treated with chymotrypsin
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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN WAS TREATED WITH CHYMOTRYPSIN AFTER PURIFICATION. THIS CLEAVED PROTEIN WAS THEN USED ...THE PROTEIN WAS TREATED WITH CHYMOTRYPSIN AFTER PURIFICATION. THIS CLEAVED PROTEIN WAS THEN USED FOR CRYSTALLIZATION.

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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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M calcium acetate, 0.1 M HEPES, pH 7.5, 40% PEG400, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 27, 2009
RadiationMonochromator: Diamond (111)and Ge (220) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3→149.071 Å / Num. all: 68562 / Num. obs: 68562 / % possible obs: 98.7 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.162.10.3991.62100099510.39998.4
3.16-3.352.10.2652.81990294540.26598.4
3.35-3.592.10.1773.21865088560.17798.9
3.59-3.872.10.1194.71732382600.11998.8
3.87-4.242.10.0871.91594176240.08798.9
4.24-4.742.10.0668.51441269340.06699
4.74-5.482.10.0569.71268661020.05699.1
5.48-6.712.10.0658.61063251760.06599.2
6.71-9.4920.0546.7812140100.05499.1
9.49-41.311.90.0536.8418521950.05396.9

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J3U

1j3u


Resolution: 3→40 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.869 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.533 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2966 3466 5.1 %RANDOM
Rwork0.2396 ---
obs0.2425 68545 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 123.96 Å2 / Biso mean: 67.3442 Å2 / Biso min: 13.67 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å20 Å2-0.5 Å2
2--2.57 Å20 Å2
3----5.33 Å2
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23922 0 2 60 23984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02224310
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216166
X-RAY DIFFRACTIONr_angle_refined_deg0.9561.96132896
X-RAY DIFFRACTIONr_angle_other_deg0.829339816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16953098
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.62425.6381082
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.084154334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.70815104
X-RAY DIFFRACTIONr_chiral_restr0.0530.23796
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02127084
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024460
X-RAY DIFFRACTIONr_mcbond_it0.4371.515450
X-RAY DIFFRACTIONr_mcbond_other0.0411.56288
X-RAY DIFFRACTIONr_mcangle_it0.797224960
X-RAY DIFFRACTIONr_scbond_it0.50938860
X-RAY DIFFRACTIONr_scangle_it0.8914.57936
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2189MEDIUM POSITIONAL0.140.5
1A2599LOOSE POSITIONAL0.285
1A2189MEDIUM THERMAL0.132
1A2599LOOSE THERMAL0.1710
2B2189MEDIUM POSITIONAL0.140.5
2B2599LOOSE POSITIONAL0.225
2B2189MEDIUM THERMAL0.132
2B2599LOOSE THERMAL0.1810
3C2189MEDIUM POSITIONAL0.130.5
3C2599LOOSE POSITIONAL0.255
3C2189MEDIUM THERMAL0.112
3C2599LOOSE THERMAL0.1610
4D2189MEDIUM POSITIONAL0.130.5
4D2599LOOSE POSITIONAL0.235
4D2189MEDIUM THERMAL0.112
4D2599LOOSE THERMAL0.1710
5G16TIGHT POSITIONAL0.030.05
5G20MEDIUM POSITIONAL0.020.5
5G16TIGHT THERMAL1.560.5
5G20MEDIUM THERMAL2.162
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 227 -
Rwork0.317 4766 -
all-4993 -
obs--97.92 %

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