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- PDB-3a54: Crystal structure of the A47Q1 mutant of pro-protein-glutaminase -

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Basic information

Entry
Database: PDB / ID: 3a54
TitleCrystal structure of the A47Q1 mutant of pro-protein-glutaminase
ComponentsProtein-glutaminase
KeywordsHYDROLASE / mutant structure like a substrate-enzyme complex
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: 1.502 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
Revision 1.3Nov 1, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Water16,340907
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)56.986, 104.113, 134.189
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.: 907 / 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: 58.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 20% PEG 3350, 0.2M ammonium tartrate, pH 6.7, 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: Dec 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 125864 / % possible obs: 98.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 17.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.7 / Num. unique all: 11528 / % possible all: 91.5

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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 3A56

3a56


Resolution: 1.502→19.894 Å / FOM work R set: 0.924 / SU ML: 0.18 / σ(F): 1.89 / Phase error: 13.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1674 6316 5.02 %
Rwork0.1398 --
obs0.1412 125753 51.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.854 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 28.492 Å2
Baniso -1Baniso -2Baniso -3
1-1.307 Å20 Å2-0 Å2
2--2.079 Å2-0 Å2
3----3.387 Å2
Refinement stepCycle: LAST / Resolution: 1.502→19.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 0 907 5211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054866
X-RAY DIFFRACTIONf_angle_d1.026711
X-RAY DIFFRACTIONf_dihedral_angle_d16.9471883
X-RAY DIFFRACTIONf_chiral_restr0.07769
X-RAY DIFFRACTIONf_plane_restr0.005875
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 (%)
1.502-1.5190.2081830.1773431361444
1.519-1.5360.2171840.1633627381146
1.536-1.5550.1952010.1493746394748
1.555-1.5750.182240.1423845406949
1.575-1.5960.1861920.1433870406250
1.596-1.6170.1761990.1353951415050
1.617-1.6410.1722070.133928413551
1.641-1.6650.1722080.1223927413551
1.665-1.6910.1562180.1163993421151
1.691-1.7190.1632090.1093977418651
1.719-1.7480.1442160.1043956417251
1.748-1.780.1462150.1074016423151
1.78-1.8140.1661950.1054010420551
1.814-1.8510.1552250.1063969419451
1.851-1.8920.1392250.1094034425951
1.892-1.9360.1471990.1073983418252
1.936-1.9840.1532200.114015423552
1.984-2.0370.1462260.1074042426852
2.037-2.0970.1471980.1054024422252
2.097-2.1650.1552130.114032424552
2.165-2.2420.1592040.1184048425252
2.242-2.3320.1542290.1174029425852
2.332-2.4380.1622050.1234057426252
2.438-2.5660.162220.134066428852
2.566-2.7270.152090.1354068427752
2.727-2.9370.1582280.1334073430152
2.937-3.2310.1652080.1394101430953
3.231-3.6960.1612210.1324120434153
3.696-4.6470.1412400.134146438653
4.647-19.8960.191930.1754353454655

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