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- PDB-4l7q: Crystal structure of gamma glutamyl hydrolase (wild-type) from ze... -

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Basic information

Entry
Database: PDB / ID: 4l7q
TitleCrystal structure of gamma glutamyl hydrolase (wild-type) from zebrafish
ComponentsGamma-glutamyl hydrolase
KeywordsHYDROLASE / sandwiched-like domains
Function / homology
Function and homology information


folate gamma-glutamyl hydrolase / tetrahydrofolylpolyglutamate metabolic process / gamma-glutamyl-peptidase activity / Neutrophil degranulation / folic acid-containing compound metabolic process / vacuole / extracellular region
Similarity search - Function
Peptidase C26, gamma-glutamyl hydrolase / Gamma-glutamyl hydrolase domain profile. / Peptidase C26 / Peptidase C26 / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
folate gamma-glutamyl hydrolase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChuankhayan, P. / Kao, T.-T. / Chen, C.-J. / Fu, T.-F.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structural insights into the hydrolysis and polymorphism of methotrexate polyglutamate by zebrafish gamma-glutamyl hydrolase
Authors: Chuankhayan, P. / Kao, T.-T. / Lin, C.-C. / Guan, H.-H. / Nakagawa, A. / Fu, T.-F. / Chen, C.-J.
History
DepositionJun 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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
C: Gamma-glutamyl hydrolase
D: Gamma-glutamyl hydrolase
A: Gamma-glutamyl hydrolase
B: Gamma-glutamyl hydrolase
E: Gamma-glutamyl hydrolase
F: Gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,05412
Polymers212,5026
Non-polymers5536
Water13,529751
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Gamma-glutamyl hydrolase
D: Gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0184
Polymers70,8342
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-6 kcal/mol
Surface area22380 Å2
MethodPISA
3
A: Gamma-glutamyl hydrolase
B: Gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0184
Polymers70,8342
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-9 kcal/mol
Surface area22370 Å2
MethodPISA
4
E: Gamma-glutamyl hydrolase
F: Gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0184
Polymers70,8342
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-7 kcal/mol
Surface area22450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)271.61, 62.05, 123.94
Angle α, β, γ (deg.)90.00, 95.4120, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Gamma-glutamyl hydrolase


Mass: 35416.961 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: ggh / Production host: Escherichia coli (E. coli)
References: UniProt: Q6NY42, folate gamma-glutamyl hydrolase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 49.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 4000, 0.1M Sodium citarte tribasic, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13C111
SYNCHROTRONSPring-8 BL12B221
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDOct 1, 2011
ADSC QUANTUM 210r2CCDApr 25, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 117219 / Num. obs: 117219 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
X-PLORmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L9X

1l9x


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.826 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.207 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 5869 5 %RANDOM
Rwork0.198 ---
all0.23 111177 --
obs0.23 111177 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.993 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.02 Å2
2--0.09 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13854 0 36 751 14641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONc_bond_d0.0230.02214261
X-RAY DIFFRACTIONc_angle_deg1.911.9519331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15751710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.95924.248678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.126152315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3521554
X-RAY DIFFRACTIONr_chiral_restr0.1560.22070
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110944
X-RAY DIFFRACTIONr_mcbond_it1.0861.58598
X-RAY DIFFRACTIONr_mcangle_it1.91213895
X-RAY DIFFRACTIONr_scbond_it3.01335663
X-RAY DIFFRACTIONr_scangle_it4.5084.55436
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 416 -
Rwork0.273 7630 -
obs--91.52 %

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