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- PDB-2faw: crystal structure of papaya glutaminyl cyclase -

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Basic information

Entry
Database: PDB / ID: 2faw
Titlecrystal structure of papaya glutaminyl cyclase
Componentsglutamine cyclotransferase
KeywordsTRANSFERASE / 5-bladed beta-propeller
Function / homologyGlutaminyl-peptide cyclotransferase / Glutamine cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / Quinoprotein amine dehydrogenase, beta chain-like / metal ion binding / ACETIC ACID / Glutamine cyclotransferase
Function and homology information
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsWintjens, R. / Belrhali, H. / Clantin, B. / Azarkan, M. / Bompard, C. / Baeyens-Volant, D. / Looze, Y. / Villeret, V.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of papaya glutaminyl cyclase, an archetype for plant and bacterial glutaminyl cyclases.
Authors: Wintjens, R. / Belrhali, H. / Clantin, B. / Azarkan, M. / Bompard, C. / Baeyens-Volant, D. / Looze, Y. / Villeret, V.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: crystallization and preliminary X-ray diffraction studies of the glutaminyl cyclase from carica papaya latex
Authors: Azarkan, M. / Clantin, C. / Bompard, C. / Belrhali, H. / Baeyens-Volant, D. / Looze, Y. / Villeret, V.
History
DepositionDec 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.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_label_asym_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glutamine cyclotransferase
B: glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5518
Polymers61,9352
Non-polymers1,6166
Water16,159897
1
A: glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8884
Polymers30,9671
Non-polymers9203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glutamine cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6634
Polymers30,9671
Non-polymers6963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.820, 81.200, 108.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological form of the protein is monomeric

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein glutamine cyclotransferase


Mass: 30967.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: latex / Source: (natural) Carica papaya (papaya) / References: UniProt: O81226

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 901 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 897 / 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: 44.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 85 mM Tris-HCl, 0.17 M sodium acetate, 25% PEG 4000, 15% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953718, 1.77122
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2004 / Details: toroidal focussing mirror
RadiationMonochromator: Chanel cut Si 111 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9537181
21.771221
ReflectionResolution: 1.7→19.537 Å / Num. all: 61500 / Num. obs: 61500 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.9 % / Rsym value: 0.06 / Net I/σ(I): 41.6
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 29.3 % / Mean I/σ(I) obs: 15.3 / Num. unique all: 9594 / Rsym value: 0.279 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT1.701data extraction
SCALEdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.537 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.853 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3075 5 %RANDOM
Rwork0.165 ---
all0.167 ---
obs-61499 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.89 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 101 897 5122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214330
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.975864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8155498
X-RAY DIFFRACTIONr_chiral_restr0.0780.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023222
X-RAY DIFFRACTIONr_nbd_refined0.2430.23823
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.21304
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.266
X-RAY DIFFRACTIONr_mcbond_it0.8891.52479
X-RAY DIFFRACTIONr_mcangle_it1.48424004
X-RAY DIFFRACTIONr_scbond_it2.01531851
X-RAY DIFFRACTIONr_scangle_it3.0274.51860
X-RAY DIFFRACTIONr_rigid_bond_restr0.98624330
X-RAY DIFFRACTIONr_sphericity_free1.8972899
X-RAY DIFFRACTIONr_sphericity_bonded1.79724225
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.222 224
Rwork0.174 4260
obs-4484

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