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- PDB-4n7d: Selenomethionine incorporated Bla g 4 -

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Basic information

Entry
Database: PDB / ID: 4n7d
TitleSelenomethionine incorporated Bla g 4
ComponentsBla g 4 allergen variant 1
KeywordsALLERGEN / beta barrel / cockroach / glycoprotein / secreted
Function / homology
Function and homology information


symbiont-mediated perturbation of host defenses / extracellular region
Similarity search - Function
Triabin/Procalin / Triabin / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Bla g 4 allergen variant 1
Similarity search - Component
Biological speciesBlattella germanica (German cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOffermann, L.R. / Chan, S.L. / Osinski, T. / Tan, Y.W. / Chew, F.T. / Sivaraman, J. / Mok, Y.K. / Minor, W. / Chruszcz, M.
CitationJournal: Mol.Immunol. / Year: 2014
Title: The major cockroach allergen Bla g 4 binds tyramine and octopamine.
Authors: Offermann, L.R. / Chan, S.L. / Osinski, T. / Tan, Y.W. / Chew, F.T. / Sivaraman, J. / Mok, Y.K. / Minor, W. / Chruszcz, M.
History
DepositionOct 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bla g 4 allergen variant 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8464
Polymers20,4701
Non-polymers3763
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bla g 4 allergen variant 1
hetero molecules

A: Bla g 4 allergen variant 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6928
Polymers40,9392
Non-polymers7536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3680 Å2
ΔGint-19 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.166, 60.166, 124.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-141-

MSE

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Components

#1: Protein Bla g 4 allergen variant 1


Mass: 20469.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blattella germanica (German cockroach) / Plasmid: pET32a modified / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B / References: UniProt: B7TYB2
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 1.5 M Sodium Citrate, 3% Acetone, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9797, 0.9799, 0.9600
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2006
RadiationMonochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97991
30.961
ReflectionResolution: 2.1→50 Å / Num. all: 51198 / Num. obs: 51198 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 23.71
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.97 / Num. unique all: 5140 / Rsym value: 0.38 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
HKL-3000phasing
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3EBK

3ebk


Resolution: 2.1→42.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.88 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.174 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21736 699 5 %RANDOM
Rwork0.1762 ---
obs0.1782 13356 99.97 %-
all-13356 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.142 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-0 Å20 Å2
2--0.28 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 25 117 1503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191460
X-RAY DIFFRACTIONr_bond_other_d00.021296
X-RAY DIFFRACTIONr_angle_refined_deg2.0311.9621986
X-RAY DIFFRACTIONr_angle_other_deg3.7743.0032964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.365179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86123.64974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14415217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2381510
X-RAY DIFFRACTIONr_chiral_restr0.120.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021690
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02360
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 47 -
Rwork0.193 964 -
obs--100 %
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)
13.2523-0.70250.70717.802-2.91735.5843-0.0984-0.2946-0.08010.3531-0.159-0.642-0.1640.67620.25730.0588-0.0189-0.06460.15640.02160.12363.0947-23.393117.3183
20.4492-0.2093-0.31491.8644-0.28410.6264-0.0534-0.016-0.0012-0.10350.0225-0.0331-0.08530.0520.0310.1831-0.0206-0.03220.03970.00630.0584-12.3099-23.512311.6643
35.4285-0.85580.94294.85071.08222.0905-0.0448-0.35280.21590.0824-0.06780.3868-0.1137-0.10630.11270.24060.0062-0.03030.11160.02120.0787-14.5605-20.743315.9677
414.7891.2803-4.3537.64080.1296.08830.2542-0.10250.56640.3115-0.15370.3278-0.2749-0.1945-0.10050.14690.0117-0.0190.0163-0.01280.0447-13.1411-18.596522.0997
51.41180.1566-1.26842.623-1.18593.4516-0.1389-0.0767-0.0495-0.0188-0.0094-0.29580.12070.21010.14830.132-0.0088-0.02890.08280.01140.0457-5.1712-27.510615.1062
67.2568-1.5183.85544.835-5.308311.7451-0.22890.42920.3137-0.12320.0850.12830.0607-0.35810.14390.1457-0.0469-0.00360.07790.0010.0387-13.5873-24.09780.2659
717.0856-7.34222.11110.3966-0.77975.59830.01690.0954-0.7699-0.53960.42450.77680.525-0.8669-0.44140.1958-0.1558-0.05390.23330.07470.0881-18.5546-31.4244-0.4199
81.44741.06920.18883.6474-1.02482.7758-0.09660.1139-0.3936-0.3432-0.0145-0.47280.23350.19130.1110.26210.0160.0790.065-0.00650.1295-3.7649-37.22226.7076
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 23
2X-RAY DIFFRACTION2A24 - 57
3X-RAY DIFFRACTION3A58 - 80
4X-RAY DIFFRACTION4A81 - 90
5X-RAY DIFFRACTION5A91 - 121
6X-RAY DIFFRACTION6A122 - 135
7X-RAY DIFFRACTION7A136 - 151
8X-RAY DIFFRACTION8A152 - 175

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