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- PDB-3a56: Crystal structure of pro- protein-glutaminase -

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Basic information

Entry
Database: PDB / ID: 3a56
TitleCrystal structure of pro- protein-glutaminase
ComponentsProtein-glutaminase
KeywordsHYDROLASE / pro-enzyme
Function / homology
Function and homology information


OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #340 / Protein glutaminase / Glutaminase / C8orf32 fold - #30 / C8orf32 fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Protein-glutaminase
Similarity search - Component
Biological speciesChryseobacterium proteolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.728 Å
AuthorsHashizume, R. / Yamaguchi, S. / Mikami, B.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structures of protein glutaminase and its pro forms converted into enzyme-substrate complex
Authors: Hashizume, R. / Maki, Y. / Mizutani, K. / Takahashi, N. / Matsubara, H. / Sugita, A. / Sato, K. / Yamaguchi, S. / Mikami, B.
History
DepositionJul 31, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3Nov 1, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-glutaminase
B: Protein-glutaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4944
Polymers67,1092
Non-polymers3842
Water13,007722
1
A: Protein-glutaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7472
Polymers33,5551
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein-glutaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7472
Polymers33,5551
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.644, 103.290, 132.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein-glutaminase / pro-protein-glutaminase


Mass: 33554.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chryseobacterium proteolyticum (bacteria)
Strain: DH5a / Gene: prgA / Plasmid: pET-20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9AQQ8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / Source method: isolated from a natural source / Formula: H2O
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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 0.2M Ammonium Citrate dibasic, 20% PEG 3350, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.728→50 Å / Num. obs: 80701 / % possible obs: 98.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.35 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.314 / Num. unique all: 7359 / % possible all: 90.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZK9

2zk9


Resolution: 1.728→30.551 Å / FOM work R set: 0.866 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 20.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 4037 5.01 %
Rwork0.1746 --
obs0.1762 80631 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 496.81 Å2 / Biso mean: 29.611 Å2 / Biso min: 4.99 Å2
Baniso -1Baniso -2Baniso -3
1-8.341 Å2-0 Å2-0 Å2
2---5.96 Å2-0 Å2
3----2.381 Å2
Refinement stepCycle: LAST / Resolution: 1.728→30.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 26 722 5064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074827
X-RAY DIFFRACTIONf_angle_d1.0676646
X-RAY DIFFRACTIONf_dihedral_angle_d17.3031848
X-RAY DIFFRACTIONf_chiral_restr0.072757
X-RAY DIFFRACTIONf_plane_restr0.005867
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.729-1.7490.2421190.2142302242187
1.749-1.770.2231380.1992420255891
1.77-1.7930.2361500.1912465261594
1.793-1.8160.2181310.1992523265495
1.816-1.8410.2481570.1972565272297
1.841-1.8670.2521410.22574271598
1.867-1.8950.251320.1912623275597
1.895-1.9250.2111370.192582271999
1.925-1.9560.2211400.1852610275098
1.956-1.990.2421310.1952621275299
1.99-2.0260.231360.1912675281199
2.026-2.0650.2141310.1852630276199
2.065-2.1070.2191400.1832633277399
2.107-2.1530.1941270.182676280399
2.153-2.2030.2481450.17726372782100
2.203-2.2580.2091550.18326682823100
2.258-2.3190.2011330.17226682801100
2.319-2.3880.1971460.1826692815100
2.388-2.4650.2261210.18627112832100
2.465-2.5530.2581470.1826652812100
2.553-2.6550.1791370.17427012838100
2.655-2.7760.2031350.16626802815100
2.776-2.9220.2041470.17226942841100
2.922-3.1050.2151410.17427282869100
3.105-3.3440.1831380.16627302868100
3.344-3.680.1861540.15327162870100
3.68-4.2110.1531370.13927462883100
4.211-5.3010.1661530.1327762929100
5.301-30.5560.21380.1862906304499

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