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- PDB-4l8f: Crystal structure of gamma-glutamyl hydrolase (C108A) complex with MTX -

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Basic information

Entry
Database: PDB / ID: 4l8f
TitleCrystal structure of gamma-glutamyl hydrolase (C108A) complex with MTX
ComponentsGamma-glutamyl hydrolase
KeywordsHYDROLASE / sandwiched-like domains / Gamma-glutamyl Hydrolase
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 / glutamine metabolic process / 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
METHOTREXATE / folate gamma-glutamyl hydrolase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 17, 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_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_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
C: Gamma-glutamyl hydrolase
D: Gamma-glutamyl hydrolase
B: Gamma-glutamyl hydrolase
A: Gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,4486
Polymers141,5404
Non-polymers9092
Water17,168953
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)71,2243
Polymers70,7702
Non-polymers4541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-9 kcal/mol
Surface area22770 Å2
MethodPISA
3
B: Gamma-glutamyl hydrolase
A: Gamma-glutamyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2243
Polymers70,7702
Non-polymers4541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-11 kcal/mol
Surface area22750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.3960, 198.0980, 65.1120
Angle α, β, γ (deg.)90.0000, 113.8160, 90.0000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Gamma-glutamyl hydrolase


Mass: 35384.898 Da / Num. of mol.: 4 / Mutation: C108A
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 / Comment: chemotherapy*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 953 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 8000, 0.1M Tris, 0.2M Magnesium chloride, pH 8.5, 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 BL13B111
SYNCHROTRONNSRRC BL13C121
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJan 10, 2012
ADSC QUANTUM 315r2CCDMay 25, 2012
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: 1.97→30 Å / Num. all: 81489 / Num. obs: 81489 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.97→2.04 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
X-PLORmodel building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L9X

1l9x


Resolution: 1.97→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.848 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.178 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23857 4309 5 %RANDOM
Rwork0.17474 ---
obs0.17799 81489 99.23 %-
all-91616 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.95 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9232 0 66 953 10251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0229562
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.95712986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46651144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55824.248452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.276151540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7531536
X-RAY DIFFRACTIONr_chiral_restr0.2070.21382
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217408
X-RAY DIFFRACTIONr_mcbond_it1.2451.55748
X-RAY DIFFRACTIONr_mcangle_it2.19629298
X-RAY DIFFRACTIONr_scbond_it3.44333814
X-RAY DIFFRACTIONr_scangle_it5.3844.53688
LS refinement shellResolution: 1.97→2.024 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 274 -
Rwork0.197 5465 -
obs--91.46 %

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