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- PDB-5hw0: Erwinia chrysanthemi L-asparaginase + Glutamic acid -

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Basic information

Entry
Database: PDB / ID: 5hw0
TitleErwinia chrysanthemi L-asparaginase + Glutamic acid
ComponentsL-asparaginase
KeywordsHYDROLASE / L-asparaginase / Erwinia chrysanthemum / Glutamic acid
Function / homology
Function and homology information


asparagine metabolic process / asparaginase / asparaginase activity
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 speciesDickeya chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.702 Å
AuthorsNguyen, H.A. / Lavie, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)RO1 EB013685 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural Insight into Substrate Selectivity of Erwinia chrysanthemi l-Asparaginase.
Authors: Nguyen, H.A. / Su, Y. / Lavie, A.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Data collection
Revision 1.2Sep 27, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,7628
Polymers141,1734
Non-polymers5894
Water18,4111022
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16020 Å2
ΔGint-35 kcal/mol
Surface area38010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.240, 88.818, 174.573
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 3:13 or (resid 16 and (name...
21(chain B and (resseq 3:13 or (resid 16 and (name...
31(chain C and (resseq 3:13 or (resid 16 and (name...
41(chain D and (resseq 3:13 or (resid 16 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLYGLY(chain A and (resseq 3:13 or (resid 16 and (name...AA3 - 134 - 14
12ILEILEILEILE(chain A and (resseq 3:13 or (resid 16 and (name...AA1617
13LYSLYSTYRTYR(chain A and (resseq 3:13 or (resid 16 and (name...AA3 - 3274 - 328
14LYSLYSTYRTYR(chain A and (resseq 3:13 or (resid 16 and (name...AA3 - 3274 - 328
15LYSLYSTYRTYR(chain A and (resseq 3:13 or (resid 16 and (name...AA3 - 3274 - 328
16LYSLYSTYRTYR(chain A and (resseq 3:13 or (resid 16 and (name...AA3 - 3274 - 328
17LYSLYSTYRTYR(chain A and (resseq 3:13 or (resid 16 and (name...AA3 - 3274 - 328
21LYSLYSGLYGLY(chain B and (resseq 3:13 or (resid 16 and (name...BB3 - 134 - 14
22ILEILEILEILE(chain B and (resseq 3:13 or (resid 16 and (name...BB1617
23LYSLYSTYRTYR(chain B and (resseq 3:13 or (resid 16 and (name...BB3 - 3274 - 328
24LYSLYSTYRTYR(chain B and (resseq 3:13 or (resid 16 and (name...BB3 - 3274 - 328
25LYSLYSTYRTYR(chain B and (resseq 3:13 or (resid 16 and (name...BB3 - 3274 - 328
26LYSLYSTYRTYR(chain B and (resseq 3:13 or (resid 16 and (name...BB3 - 3274 - 328
27LYSLYSTYRTYR(chain B and (resseq 3:13 or (resid 16 and (name...BB3 - 3274 - 328
31LYSLYSGLYGLY(chain C and (resseq 3:13 or (resid 16 and (name...CC3 - 134 - 14
32ILEILEILEILE(chain C and (resseq 3:13 or (resid 16 and (name...CC1617
33LYSLYSTYRTYR(chain C and (resseq 3:13 or (resid 16 and (name...CC3 - 3274 - 328
34LYSLYSTYRTYR(chain C and (resseq 3:13 or (resid 16 and (name...CC3 - 3274 - 328
35LYSLYSTYRTYR(chain C and (resseq 3:13 or (resid 16 and (name...CC3 - 3274 - 328
36LYSLYSTYRTYR(chain C and (resseq 3:13 or (resid 16 and (name...CC3 - 3274 - 328
37LYSLYSTYRTYR(chain C and (resseq 3:13 or (resid 16 and (name...CC3 - 3274 - 328
41LYSLYSGLYGLY(chain D and (resseq 3:13 or (resid 16 and (name...DD3 - 134 - 14
42ILEILEILEILE(chain D and (resseq 3:13 or (resid 16 and (name...DD1617
43LYSLYSTYRTYR(chain D and (resseq 3:13 or (resid 16 and (name...DD3 - 3274 - 328
44LYSLYSTYRTYR(chain D and (resseq 3:13 or (resid 16 and (name...DD3 - 3274 - 328
45LYSLYSTYRTYR(chain D and (resseq 3:13 or (resid 16 and (name...DD3 - 3274 - 328
46LYSLYSTYRTYR(chain D and (resseq 3:13 or (resid 16 and (name...DD3 - 3274 - 328
47LYSLYSTYRTYR(chain D and (resseq 3:13 or (resid 16 and (name...DD3 - 3274 - 328

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Components

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


Mass: 35293.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Gene: ansB, asn / Plasmid: pET-14b modified / Details (production host): with His-SUMO tag / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P06608, asparaginase
#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1022 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 24% PEG MME 2000

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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: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 128606 / % possible obs: 99.3 % / Redundancy: 7.38 % / Biso Wilson estimate: 23.36 Å2 / CC1/2: 0.999 / Rsym value: 0.081 / Net I/σ(I): 19.62
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.55 / % possible all: 96

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata scaling
XDSdata reduction
PDB_EXTRACT3.2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O7J

1o7j


Resolution: 1.702→28.763 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.13
RfactorNum. reflection% reflection
Rfree0.2054 6289 4.94 %
Rwork0.1665 --
obs0.1684 127190 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.18 Å2 / Biso mean: 19.4703 Å2 / Biso min: 5.3 Å2
Refinement stepCycle: final / Resolution: 1.702→28.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9494 0 45 1022 10561
Biso mean--24.38 28.32 -
Num. residues----1255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069853
X-RAY DIFFRACTIONf_angle_d0.84313390
X-RAY DIFFRACTIONf_chiral_restr0.061589
X-RAY DIFFRACTIONf_plane_restr0.0061739
X-RAY DIFFRACTIONf_dihedral_angle_d11.5415986
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5122X-RAY DIFFRACTION4.254TORSIONAL
12B5122X-RAY DIFFRACTION4.254TORSIONAL
13C5122X-RAY DIFFRACTION4.254TORSIONAL
14D5122X-RAY DIFFRACTION4.254TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7023-1.72160.32731850.29433660384591
1.7216-1.74190.33712070.28940644271100
1.7419-1.76310.3112310.280340084239100
1.7631-1.78540.31491960.279440194215100
1.7854-1.80890.30052250.264140074232100
1.8089-1.83370.29732190.261640274246100
1.8337-1.85990.29492020.244140464248100
1.8599-1.88760.25532330.223340104243100
1.8876-1.91710.29562280.220739804208100
1.9171-1.94850.25292010.20240194220100
1.9485-1.98210.23412070.199340914298100
1.9821-2.01820.25072050.195340034208100
2.0182-2.0570.24892130.193140414254100
2.057-2.09890.23282020.188540524254100
2.0989-2.14460.22461850.180340484233100
2.1446-2.19440.20611960.16740504246100
2.1944-2.24930.21732060.161540204226100
2.2493-2.31010.19512080.15394058426699
2.3101-2.3780.19192260.152540384264100
2.378-2.45470.19932300.153240134243100
2.4547-2.54240.19222080.154063427199
2.5424-2.64420.18912020.15274063426599
2.6442-2.76440.21082050.1494039424499
2.7644-2.910.20011940.14434068426299
2.91-3.09210.17041940.14214024421899
3.0921-3.33060.18752160.14024038425498
3.3306-3.66510.17282260.13324005423198
3.6651-4.19410.14621980.12574048424697
4.1941-5.27880.15682230.12494049427297
5.2788-28.76740.16622180.1584250446897

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