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- PDB-4rld: Crystal structure of kkf mutant of bla G 2 protein -

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Basic information

Entry
Database: PDB / ID: 4rld
TitleCrystal structure of kkf mutant of bla G 2 protein
ComponentsAspartic protease Bla g 2
KeywordsHYDROLASE / Bla G 2 / Allegen
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / aspartic-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Immunoglobulin-like - #1960 / Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase domain superfamily / Immunoglobulin-like ...Immunoglobulin-like - #1960 / Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase domain superfamily / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Aspartic protease Bla g 2
Similarity search - Component
Biological speciesBlattella germanica (German cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsLi, M. / Gustchina, A. / Pomes, A. / Wlodawer, A.
CitationJournal: To be Published
Title: to be determined
Authors: Li, M. / Gustchina, A. / Pomes, A. / Wlodawer, A.
History
DepositionOct 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / chem_comp ...atom_site / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
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: Aspartic protease Bla g 2
B: Aspartic protease Bla g 2
C: Aspartic protease Bla g 2
D: Aspartic protease Bla g 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,22912
Polymers144,2704
Non-polymers1,9598
Water64936
1
A: Aspartic protease Bla g 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5573
Polymers36,0681
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aspartic protease Bla g 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5573
Polymers36,0681
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aspartic protease Bla g 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5573
Polymers36,0681
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Aspartic protease Bla g 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5573
Polymers36,0681
Non-polymers4902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Aspartic protease Bla g 2
B: Aspartic protease Bla g 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1156
Polymers72,1352
Non-polymers9804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-16 kcal/mol
Surface area27660 Å2
MethodPISA
6
C: Aspartic protease Bla g 2
D: Aspartic protease Bla g 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1156
Polymers72,1352
Non-polymers9804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-13 kcal/mol
Surface area28180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.819, 75.410, 339.852
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Aspartic protease Bla g 2 / Allergen Bla g II


Mass: 36067.539 Da / Num. of mol.: 4 / Fragment: Bla G 2 / Mutation: K132A, K251A and F162Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blattella germanica (German cockroach) / Plasmid: PGAPZAC / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115
References: UniProt: P54958, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#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.: 4
Source method: isolated from a genetically manipulated source
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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG8k, 0.2 M Mg Acetate, 10mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 20, 2010
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 39171 / Num. obs: 34481 / % possible obs: 88.5 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rsym value: 0.086 / Net I/σ(I): 14
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.5 % / Num. unique all: 1730 / Rsym value: 0.298 / % possible all: 45.3

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Processing

Software
NameVersionClassification
MAR345serguidata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.861 / SU B: 35.02 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25674 1074 3.1 %RANDOM
Rwork0.19588 ---
obs0.19775 33408 88.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.338 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20 Å2
2--2.22 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10156 0 116 36 10308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210540
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9514352
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4551316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14625.21476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.814151640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9721528
X-RAY DIFFRACTIONr_chiral_restr0.0790.21624
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218040
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5561.56528
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.092210588
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.42534012
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6054.53764
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 35 -
Rwork0.29 1123 -
obs--41.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.97520.47320.27481.3210.10840.94270.05890.1120.01560.2220.05370.1473-0.0692-0.0894-0.11260.08190.02880.0660.03290.02630.057124.267511.231483.1002
21.2604-0.0730.21350.67450.01492.1928-0.00730.1037-0.0513-0.15250.0867-0.10960.11850.0716-0.07950.0939-0.03710.05280.0748-0.02380.047644.28971.437351.7287
32.01760.3550.65491.29681.01832.06030.0026-0.2295-0.11760.0092-0.0230.01540.15120.30640.02040.14350.01750.04920.31250.04290.029947.90315.54949.9569
41.50181.77430.60255.53342.30462.2653-0.0826-0.1530.30390.0292-0.10660.5824-0.3355-0.10680.18920.29330.0561-0.02020.2084-0.0380.146924.34430.743326.7076
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-8 - 327
2X-RAY DIFFRACTION2B-8 - 327
3X-RAY DIFFRACTION3C-8 - 327
4X-RAY DIFFRACTION4D-8 - 327

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