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- PDB-6nxc: ECAI(T162A) MUTANT IN COMPLEX WITH CITRATE AT PH 4 -

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Basic information

Entry
Database: PDB / ID: 6nxc
TitleECAI(T162A) MUTANT IN COMPLEX WITH CITRATE AT PH 4
ComponentsL-asparaginase 1
KeywordsHYDROLASE / hydrolysis of L-asparagine
Function / homology
Function and homology information


L-asparagine catabolic process via L-aspartate / asparaginase / asparaginase activity / protein homotetramerization / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / 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 ...Type I L-asparaginase family / Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / 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
ASPARAGINE / CITRIC ACID / L-asparaginase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.74 Å
AuthorsLubkowski, J. / Wlodawer, A.
CitationJournal: J. Mol. Biol. / Year: 2007
Title: Crystal structure and allosteric regulation of the cytoplasmic Escherichia coli L-asparaginase I.
Authors: Yun, M.K. / Nourse, A. / White, S.W. / Rock, C.O. / Heath, R.J.
History
DepositionFeb 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0THIS ENTRY 6NXC REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R2HIMSF ORIGINAL DATA ...THIS ENTRY 6NXC REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R2HIMSF ORIGINAL DATA DETERMINED BY AUTHOR: M.K.YUN,A.NOURSE,S.W.WHITE,C.O.ROCK,R.J.HEATH.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-asparaginase 1
B: L-asparaginase 1
C: L-asparaginase 1
D: L-asparaginase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,18834
Polymers156,7614
Non-polymers2,42630
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18880 Å2
ΔGint-103 kcal/mol
Surface area43860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.524, 89.766, 93.290
Angle α, β, γ (deg.)90.000, 117.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 39190.348 Da / Num. of mol.: 4 / Mutation: T162A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ansA, b1767, JW1756 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A962, asparaginase

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Non-polymers , 6 types, 595 molecules

#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8N2O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.67 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2HIM
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Citrate buffer, Sodium Chloride, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97923 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 132353 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Net I/σ(I): 14.8
Reflection shellResolution: 1.74→1.81 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.74→46.54 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.236 / SU ML: 0.072 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.113
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 6415 5.1 %RANDOM
Rwork0.166 ---
obs0.1681 120380 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.73 Å2 / Biso mean: 25.698 Å2 / Biso min: 11.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å2-0.03 Å2
2---0.43 Å20 Å2
3---0.38 Å2
Refinement stepCycle: final / Resolution: 1.74→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10128 0 135 565 10828
Biso mean--26.66 31.89 -
Num. residues----1320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01310489
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179667
X-RAY DIFFRACTIONr_angle_refined_deg2.2561.64814249
X-RAY DIFFRACTIONr_angle_other_deg1.5981.56722462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.53751307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21822.934518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.159151675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3491556
X-RAY DIFFRACTIONr_chiral_restr0.1150.21395
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022018
LS refinement shellResolution: 1.744→1.79 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 321 -
Rwork0.234 6369 -
all-6690 -
obs--67.42 %

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