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- PDB-3a55: Crystal structure of the A47Q2 mutant of pro- protein-glutaminase -

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Basic information

Entry
Database: PDB / ID: 3a55
TitleCrystal structure of the A47Q2 mutant of pro- protein-glutaminase
ComponentsProtein-glutaminase
KeywordsHYDROLASE / mutant structure like the reaction intermediate
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
Biological speciesChryseobacterium proteolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 30, 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 / Derived calculations
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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 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


Theoretical massNumber of molelcules
Total (without water)67,2242
Polymers67,2242
Non-polymers00
Water15,079837
1
A: Protein-glutaminase


Theoretical massNumber of molelcules
Total (without water)33,6121
Polymers33,6121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein-glutaminase


Theoretical massNumber of molelcules
Total (without water)33,6121
Polymers33,6121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.134, 103.792, 134.100
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: 33611.750 Da / Num. of mol.: 2 / Mutation: A47Q
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 837 / 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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 20% PEG 3350, 0.2M sodium tartrate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.8 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 119408 / % possible obs: 93.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 14.99 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 39.27
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.332 / Num. unique all: 6016 / % possible all: 96.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A56

3a56


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.497 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 6001 5 %RANDOM
Rwork0.1574 ---
obs0.15856 113341 93.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.601 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20 Å2
2--0.86 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 0 837 5139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224699
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.9596462
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4435667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20124.894188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24615830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1281518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023568
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.22423
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.23340
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2618
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8231.53035
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.90324898
X-RAY DIFFRACTIONr_scbond_it2.89231848
X-RAY DIFFRACTIONr_scangle_it4.2684.51510
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 433 -
Rwork0.19 8232 -
obs--93.11 %

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