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- PDB-5k4h: Wolinella succinogenes L-asparaginase S121 + L-Glutamic acid -

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Basic information

Entry
Database: PDB / ID: 5k4h
TitleWolinella succinogenes L-asparaginase S121 + L-Glutamic acid
ComponentsL-asparaginase
KeywordsHYDROLASE / L-asparaginase / S121 / L-glutamic acid
Function / homology
Function and homology information


asparagine metabolic process / asparaginase / asparaginase activity / cytoplasm
Similarity search - Function
L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. ...L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like / L-asparaginase, N-terminal / Asparaginase/glutaminase-like superfamily / L-asparaginase, N-terminal domain superfamily / Asparaginase, N-terminal / Asparaginase / glutaminase domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / L-asparaginase
Similarity search - Component
Biological speciesWolinella succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNguyen, H.A. / Lave, A.
Citation
Journal: Sci Rep / Year: 2017
Title: The differential ability of asparagine and glutamine in promoting the closed/active enzyme conformation rationalizes the Wolinella succinogenes L-asparaginase substrate specificity.
Authors: Nguyen, H.A. / Durden, D.L. / Lavie, A.
#1: Journal: Biochemistry / Year: 2016
Title: Structural Insight into Substrate Selectivity of Erwinia chrysanthemi l-Asparaginase.
Authors: Nguyen, H.A. / Su, Y. / Lavie, A.
History
DepositionMay 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase
B: L-asparaginase
C: L-asparaginase
D: L-asparaginase
E: L-asparaginase
F: L-asparaginase
G: L-asparaginase
H: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,32716
Polymers279,1508
Non-polymers1,1778
Water28,2301567
1
A: L-asparaginase
B: L-asparaginase
C: L-asparaginase
D: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,1638
Polymers139,5754
Non-polymers5894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14930 Å2
ΔGint-64 kcal/mol
Surface area39650 Å2
MethodPISA
2
E: L-asparaginase
F: L-asparaginase
G: L-asparaginase
H: L-asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,1638
Polymers139,5754
Non-polymers5894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14900 Å2
ΔGint-65 kcal/mol
Surface area40310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.538, 84.181, 120.547
Angle α, β, γ (deg.)87.220, 77.760, 70.840
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 3 - 330 / Label seq-ID: 3 - 330

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213HH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218HH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222HH
123EE
223FF
124EE
224GG
125EE
225HH
126FF
226GG
127FF
227HH
128GG
228HH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
L-asparaginase / L-ASNase / L-asparagine amidohydrolase


Mass: 34893.703 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W) (bacteria)
Strain: ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W
Gene: ansA, ansB, WS0660 / Production host: Escherichia coli (E. coli) / References: UniProt: P50286, asparaginase
#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1567 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG2000 + HEPES 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. obs: 148378 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 1.98 % / Biso Wilson estimate: 35.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.85
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.99-2.110.4941.69192.6
2.11-2.260.3162.67195.9
2.26-2.440.1954.34195.9
2.44-2.670.1256.53196.1
2.67-2.980.07510.55195.3
2.98-3.440.04217.66193.6
3.44-4.20.02329.51191.7
4.2-5.870.01737.03192.1
5.87-29.3530.01442.11193.8

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
Cootmodel building
MOLREPphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WSA

1wsa


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.651 / SU ML: 0.163 / SU R Cruickshank DPI: 0.2283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.176
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 7436 5.1 %RANDOM
Rwork0.181 ---
obs0.183 139793 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 139.38 Å2 / Biso mean: 36.885 Å2 / Biso min: 15.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0.12 Å2-0.76 Å2
2---1.17 Å2-0.04 Å2
3---1.41 Å2
Refinement stepCycle: final / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19163 0 90 1567 20820
Biso mean--47.72 38.02 -
Num. residues----2580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01919528
X-RAY DIFFRACTIONr_bond_other_d0.0080.0219312
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.96826467
X-RAY DIFFRACTIONr_angle_other_deg1.449344479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02852573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.96225.712723
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.869153433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4811572
X-RAY DIFFRACTIONr_chiral_restr0.0920.23228
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0222115
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023965
X-RAY DIFFRACTIONr_mcbond_it2.8013.45910358
X-RAY DIFFRACTIONr_mcbond_other2.83.45910357
X-RAY DIFFRACTIONr_mcangle_it3.9875.17912909
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A402300.06
12B402300.06
21A397140.05
22C397140.05
31A401540.04
32D401540.04
41A402720.05
42E402720.05
51A404780.05
52F404780.05
61A406540.06
62G406540.06
71A408100.05
72H408100.05
81B399000.06
82C399000.06
91B402120.05
92D402120.05
101B403700.06
102E403700.06
111B403720.06
112F403720.06
121B403680.05
122G403680.05
131B402820.06
132H402820.06
141C401940.05
142D401940.05
151C402280.05
152E402280.05
161C401620.05
162F401620.05
171C401180.05
172G401180.05
181C402120.04
182H402120.04
191D403600.05
192E403600.05
201D403040.05
202F403040.05
211D402140.05
212G402140.05
221D402340.05
222H402340.05
231E405400.04
232F405400.04
241E404880.04
242G404880.04
251E402620.06
252H402620.06
261F404340.05
262G404340.05
271F404320.06
272H404320.06
281G403860.05
282H403860.05
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 519 -
Rwork0.345 10085 -
all-10604 -
obs--91.18 %

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