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- PDB-1l9x: Structure of gamma-Glutamyl Hydrolase -

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Basic information

Entry
Database: PDB / ID: 1l9x
TitleStructure of gamma-Glutamyl Hydrolase
Componentsgamma-glutamyl hydrolase
KeywordsHYDROLASE / gamma-glutamyl hydrolase
Function / homology
Function and homology information


folate gamma-glutamyl hydrolase / tetrahydrofolylpolyglutamate metabolic process / gamma-glutamyl-peptidase activity / exopeptidase activity / vacuole / specific granule lumen / azurophil granule lumen / melanosome / tertiary granule lumen / omega peptidase activity ...folate gamma-glutamyl hydrolase / tetrahydrofolylpolyglutamate metabolic process / gamma-glutamyl-peptidase activity / exopeptidase activity / vacuole / specific granule lumen / azurophil granule lumen / melanosome / tertiary granule lumen / omega peptidase activity / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / nucleus
Similarity search - Function
Peptidase C26, gamma-glutamyl hydrolase / Gamma-glutamyl hydrolase domain profile. / Peptidase C26 / Peptidase C26 / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Gamma-glutamyl hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsLi, H. / Ryan, T.J. / Chave, K.J. / Van Roey, P.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Three-dimensional structure of human gamma -glutamyl hydrolase. A class I glatamine amidotransferase adapted for a complex substate.
Authors: Li, H. / Ryan, T.J. / Chave, K.J. / Van Roey, P.
History
DepositionMar 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 7, 2021Group: Database references / Derived calculations / Category: struct_conn / struct_ref_seq_dif / struct_site
Item: _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag ..._struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: gamma-glutamyl hydrolase
B: gamma-glutamyl hydrolase
C: gamma-glutamyl hydrolase
D: gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,42510
Polymers143,9564
Non-polymers4696
Water14,772820
1
A: gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0672
Polymers35,9891
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1453
Polymers35,9891
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1453
Polymers35,9891
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0672
Polymers35,9891
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.763, 156.451, 161.376
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
gamma-glutamyl hydrolase


Mass: 35988.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: Q92820, folate gamma-glutamyl hydrolase
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 820 / 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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4000, ammonium acetate, sodium chloride, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 288.K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19-13 %PEG40001reservoir
20.05-0.2 Mammonium acetate1reservoir
30.1-0.2 M1reservoirNaCl
40.08 Msodium citrate1reservoirpH5.6
53.5 mg/mlprotein1drop
650 mM1dropNaAc
750 mMbeta-mercaptoethanol1drop
81 mMoctyl beta-glucopyranoside1drop
9500 mM1dropNaClpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.00918, 1.00870, 1.0064, 0.9918
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jun 3, 2001
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.009181
21.00871
31.00641
40.99181
ReflectionResolution: 1.6→25 Å / Num. all: 161629 / Num. obs: 161520 / % possible obs: 82.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 53
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 4.4 / Num. unique all: 6118 / Rsym value: 0.211 / % possible all: 31.5
Reflection
*PLUS
Redundancy: 6.3 % / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 31.5 % / Rmerge(I) obs: 0.211

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.201 8095 -RANDOM
Rwork0.181 ---
all0.181 161629 --
obs0.181 161520 82.3 %-
Displacement parametersBiso mean: 24.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9526 0 24 820 10370
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.76
Refinement
*PLUS
Lowest resolution: 100 Å / Rfactor obs: 0.182 / Rfactor Rfree: 0.202 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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