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Entry
Database: PDB / ID: 2oot
TitleA High Resolution Structure of Ligand-free Human Glutamate Carboxypeptidase II
ComponentsGlutamate carboxypeptidase 2
KeywordsHYDROLASE / metallopeptidase / folate hydrolase / prostate-specific membrane antigen / Naaladase / GCPII
Function / homology
Function and homology information


Ac-Asp-Glu binding / tetrahydrofolyl-poly(glutamate) polymer binding / glutamate carboxypeptidase II / folic acid-containing compound metabolic process / C-terminal protein deglutamylation / Aspartate and asparagine metabolism / dipeptidase activity / metallocarboxypeptidase activity / carboxypeptidase activity / peptidase activity ...Ac-Asp-Glu binding / tetrahydrofolyl-poly(glutamate) polymer binding / glutamate carboxypeptidase II / folic acid-containing compound metabolic process / C-terminal protein deglutamylation / Aspartate and asparagine metabolism / dipeptidase activity / metallocarboxypeptidase activity / carboxypeptidase activity / peptidase activity / cell surface / proteolysis / extracellular exosome / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Transcription Elongation Factor S-II; Chain A ...Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Transcription Elongation Factor S-II; Chain A / Glucose Oxidase; domain 1 / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(bba) Sandwich / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutamate carboxypeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier / Resolution: 1.64 Å
AuthorsBarinka, C. / Lubkowski, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: A high-resolution structure of ligand-free human glutamate carboxypeptidase II.
Authors: Barinka, C. / Starkova, J. / Konvalinka, J. / Lubkowski, J.
History
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate carboxypeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,54812
Polymers79,8591
Non-polymers2,68911
Water10,088560
1
A: Glutamate carboxypeptidase 2
hetero molecules

A: Glutamate carboxypeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,09524
Polymers159,7182
Non-polymers5,37722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area11650 Å2
ΔGint-127 kcal/mol
Surface area49280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.759, 130.128, 158.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsBiological assembly of GCPII is a dimer. There is one molecule in the asymetric unit. The dimer is formed via the '-x; 1-y; z" symmetry operation

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutamate carboxypeptidase 2 / Glutamate carboxypeptidase II / Membrane glutamate carboxypeptidase / mGCP / N- acetylated-alpha- ...Glutamate carboxypeptidase II / Membrane glutamate carboxypeptidase / mGCP / N- acetylated-alpha-linked acidic dipeptidase I / NAALADase I / Pteroylpoly-gamma-glutamate carboxypeptidase / Folylpoly-gamma- glutamate carboxypeptidase / FGCP / Folate hydrolase 1 / Prostate- specific membrane antigen / PSMA / PSM


Mass: 79859.031 Da / Num. of mol.: 1 / Fragment: residues 44-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOLH1, FOLH, NAALAD1, PSM, PSMA / Plasmid: pMT/BiP/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider's S2 cells / References: UniProt: Q04609, glutamate carboxypeptidase II

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Sugars , 3 types, 7 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 564 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 33% (v/v) pentaerythritol propoxylate PO/OH 5/4, 13% (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 126082 / Num. obs: 126082 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 19.7
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.6 / Num. unique all: 11591 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Difference Fourier
Starting model: PDB ENTRY 2C6G

2c6g


Resolution: 1.64→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.93 / SU ML: 0.066 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22841 3784 3 %RANDOM
Rwork0.20623 ---
obs0.20693 121530 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.292 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2---1.72 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.64→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5459 0 166 560 6185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226142
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.9878378
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9585752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20723.75280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06315978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5391535
X-RAY DIFFRACTIONr_chiral_restr0.1230.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024758
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.23148
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.24248
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2538
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.060.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2021.53734
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82425934
X-RAY DIFFRACTIONr_scbond_it2.77232724
X-RAY DIFFRACTIONr_scangle_it4.1554.52444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free9.95234
X-RAY DIFFRACTIONr_sphericity_bonded7.383321
LS refinement shellResolution: 1.642→1.685 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 240 -
Rwork0.293 7932 -
obs--87.21 %

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