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- PDB-4l8w: Crystal structure of gamma glutamyl hydrolase (H218N) from zebraf... -

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Basic information

Entry
Database: PDB / ID: 4l8w
TitleCrystal structure of gamma glutamyl hydrolase (H218N) from zebrafish complex with MTX polyglutamate
ComponentsGamma-glutamyl hydrolase
KeywordsHYDROLASE / Sandwiched-like domain
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
D-GLUTAMIC ACID / METHOTREXATE / folate gamma-glutamyl hydrolase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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 18, 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_conn / struct_ref_seq_dif / struct_site
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 / _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
D: Gamma-glutamyl hydrolase
I: Gamma-glutamyl hydrolase
B: Gamma-glutamyl hydrolase
E: Gamma-glutamyl hydrolase
G: Gamma-glutamyl hydrolase
K: Gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,85512
Polymers212,3586
Non-polymers1,4976
Water6,936385
1


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


Theoretical massNumber of molelcules
Total (without water)70,7862
Polymers70,7862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-9 kcal/mol
Surface area22990 Å2
MethodPISA
3
I: Gamma-glutamyl hydrolase
E: Gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5355
Polymers70,7862
Non-polymers7493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-9 kcal/mol
Surface area22700 Å2
MethodPISA
4
B: Gamma-glutamyl hydrolase
G: Gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5355
Polymers70,7862
Non-polymers7493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-8 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.591, 60.409, 157.055
Angle α, β, γ (deg.)90.00, 100.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Gamma-glutamyl hydrolase


Mass: 35392.918 Da / Num. of mol.: 6 / Mutation: H218N
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-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N8O5
#3: Chemical
ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 3350, 8% Tassimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jun 10, 2012
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→30 Å / Num. all: 82119 / Num. obs: 82119 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.39→2.47 Å / % possible all: 99

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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: 2.39→29.63 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.831 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.393 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25756 4102 5 %RANDOM
Rwork0.19296 ---
all0.2 78013 --
obs0.19621 78013 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-1.79 Å2
2--0.66 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.39→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13842 0 102 385 14329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02214326
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.95719448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28351716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.76224.336678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.233152316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4791554
X-RAY DIFFRACTIONr_chiral_restr0.1450.22078
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02111088
X-RAY DIFFRACTIONr_mcbond_it0.9941.58616
X-RAY DIFFRACTIONr_mcangle_it1.851213940
X-RAY DIFFRACTIONr_scbond_it2.7735710
X-RAY DIFFRACTIONr_scangle_it4.4514.55508
LS refinement shellResolution: 2.386→2.448 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 253 -
Rwork0.229 5153 -
obs--88.62 %

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