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- PDB-1u60: MCSG APC5046 Probable glutaminase ybaS -

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Basic information

Entry
Database: PDB / ID: 1u60
TitleMCSG APC5046 Probable glutaminase ybaS
ComponentsProbable glutaminase ybaS
KeywordsHYDROLASE / structural genomics / APC5046 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


glutamine catabolic process / glutamate biosynthetic process / negative regulation of growth / glutaminase / glutaminase activity / response to acidic pH / protein-containing complex
Similarity search - Function
Glutaminase / Glutaminase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Glutaminase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsChang, C. / Cuff, M.E. / Joachimiak, A. / Savchenko, A. / Edwards, A. / Skarina, T. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Biochemistry / Year: 2008
Title: Functional and structural characterization of four glutaminases from Escherichia coli and Bacillus subtilis.
Authors: Brown, G. / Singer, A. / Proudfoot, M. / Skarina, T. / Kim, Y. / Chang, C. / Dementieva, I. / Kuznetsova, E. / Gonzalez, C.F. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F.
History
DepositionJul 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Sep 26, 2012Group: Structure summary
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable glutaminase ybaS
B: Probable glutaminase ybaS
C: Probable glutaminase ybaS
D: Probable glutaminase ybaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,86425
Polymers131,7054
Non-polymers1,15921
Water20,7171150
1
A: Probable glutaminase ybaS
B: Probable glutaminase ybaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,62516
Polymers65,8522
Non-polymers77314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint0 kcal/mol
Surface area21680 Å2
MethodPISA
2
C: Probable glutaminase ybaS
D: Probable glutaminase ybaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2399
Polymers65,8522
Non-polymers3867
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-10 kcal/mol
Surface area21350 Å2
MethodPISA
3
A: Probable glutaminase ybaS
B: Probable glutaminase ybaS
hetero molecules

C: Probable glutaminase ybaS
D: Probable glutaminase ybaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,86425
Polymers131,7054
Non-polymers1,15921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area12490 Å2
ΔGint-38 kcal/mol
Surface area40080 Å2
MethodPISA
4
A: Probable glutaminase ybaS
B: Probable glutaminase ybaS
hetero molecules

C: Probable glutaminase ybaS
D: Probable glutaminase ybaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,86425
Polymers131,7054
Non-polymers1,15921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area10220 Å2
ΔGint-7 kcal/mol
Surface area42350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.509, 155.891, 164.171
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
Probable glutaminase ybaS


Mass: 32926.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ybaS / Production host: Escherichia coli (E. coli) / References: UniProt: P77454, glutaminase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1150 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growpH: 7.5
Details: crystallization solution: 0.1M Hepes, 10% isopropanol, 20% PEG 4000. Cryoprotectant: crystallization solution plus 12% Ethylene glycol, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97978 Å
DetectorType: CUSTOM-MADE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97978 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 131904 / % possible obs: 77.9 %
Reflection shellResolution: 1.61→1.67 Å / % possible all: 23

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→40 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.856 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17761 6641 5 %RANDOM
Rwork0.14295 ---
all0.14468 ---
obs0.14468 125216 78.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---1.68 Å20 Å2
3---2.38 Å2
Refinement stepCycle: LAST / Resolution: 1.61→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9216 0 75 1150 10441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0219490
X-RAY DIFFRACTIONr_bond_other_d0.0020.028541
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.95912897
X-RAY DIFFRACTIONr_angle_other_deg0.925319874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0151252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.21476
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210818
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021766
X-RAY DIFFRACTIONr_nbd_refined0.2340.22117
X-RAY DIFFRACTIONr_nbd_other0.2480.210300
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.25389
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2813
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.2124
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8771.56156
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50729790
X-RAY DIFFRACTIONr_scbond_it2.90233334
X-RAY DIFFRACTIONr_scangle_it4.5564.53097
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.655 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.261 160
Rwork0.204 2786
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.35840.05320.11490.37680.02480.14690.0013-0.00560.0006-0.0231-0.02420.00910-0.00760.02290.03590.0056-0.00160.0502-0.01770.017411.09255.4450.181
20.3782-0.11470.05450.26810.0760.2313-0.0329-0.00410.00230.04660.00860.00820.00090.02980.02430.05170.0011-0.01140.0460.01050.008524.31860.0679.19
30.44330.1407-0.05280.44150.14940.0791-0.0751-0.03610.0074-0.10240.03390.009-0.0270.01660.04120.0637-0.0056-0.00420.03570.01340.005149.49323.575.244
40.3206-0.0972-0.12150.3790.09020.1867-0.0210.0238-0.00710.0283-0.04060.0250.0086-0.02660.06160.03020.0031-0.00430.0529-0.02910.024136.44224.90134.609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 3102 - 310
2X-RAY DIFFRACTION2BB2 - 3102 - 310
3X-RAY DIFFRACTION3CC2 - 3102 - 310
4X-RAY DIFFRACTION4DD2 - 3102 - 310

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