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- PDB-4jrb: Structure of Cockroach Allergen Bla g 1 Tandem Repeat as a EGFP fusion -

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Basic information

Entry
Database: PDB / ID: 4jrb
TitleStructure of Cockroach Allergen Bla g 1 Tandem Repeat as a EGFP fusion
ComponentsGreen fluorescent protein
KeywordsLIPID BINDING PROTEIN / Allergen / asthma / new fold / proposed lipid binding protein
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Insect allergen-related / Insect allergen related repeat, nitrile-specifier detoxification / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DODECANE / Chem-PGT / Green fluorescent protein / Major allergen Bla g 1.0101
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Blattella germanica (German cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.414 Å
AuthorsMueller, G.A. / Pedersen, L.C. / Lih, F.B. / Glesner, J. / Moon, A.F. / Chapman, M.D. / Tomer, K. / London, R.E.
CitationJournal: J.Allergy Clin.Immunol. / Year: 2013
Title: The novel structure of the cockroach allergen Bla g 1 has implications for allergenicity and exposure assessment.
Authors: Mueller, G.A. / Pedersen, L.C. / Lih, F.B. / Glesner, J. / Moon, A.F. / Chapman, M.D. / Tomer, K.B. / London, R.E. / Pomes, A.
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Dec 25, 2013Group: Database references
Revision 1.4Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / struct_ref_seq_dif / Item: _entity.pdbx_description
Revision 1.5Sep 20, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 1.6Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,58310
Polymers46,7391
Non-polymers1,8449
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.768, 141.920, 93.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1401-

HOH

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Components

#1: Protein Green fluorescent protein /


Mass: 46738.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: designed off of pET28a to include a 6HIS-EGFP fusion at the N-terminus with a AAA linker region in between the EGFP and the Blag1
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Blattella germanica (German cockroach)
Gene: GFP / Plasmid: pEGFPX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3-RIL / References: UniProt: P42212, UniProt: Q9UAM5
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT) / Phosphatidylglycerol


Mass: 751.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#4: Chemical
ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H26
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND DENOTED ADS D12 IS AN UNKNOWN FATTY ACID, WITH THE CLOSEST MATCH ON OBSERVED ATOMS TO ...THE LIGAND DENOTED ADS D12 IS AN UNKNOWN FATTY ACID, WITH THE CLOSEST MATCH ON OBSERVED ATOMS TO DODECANE. THE LIGAND DENOTED AS PGT IS AN UNKNOWN PHOSPHOLIPID. OTHER STUDIES SUGGEST IT IS LIKELY A PHOSPHATIDYL GLYCEROL FROM BACTERIA

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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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM Tris, 10% propanol, 20% PEG4K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2012
RadiationMonochromator: si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 23505 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.9
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1087 / % possible all: 94

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Processing

Software
NameVersionClassification
SERGUIdata collection
MLPHAREphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AI4

3ai4


Resolution: 2.414→25.188 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1130 5.03 %random
Rwork0.1976 ---
all0.2 23505 --
obs0.2001 22483 94.48 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.53 Å2 / ksol: 0.308 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4782 Å20 Å2-0 Å2
2--7.7264 Å2-0 Å2
3----7.2482 Å2
Refinement stepCycle: LAST / Resolution: 2.414→25.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3110 0 93 100 3303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073258
X-RAY DIFFRACTIONf_angle_d1.084399
X-RAY DIFFRACTIONf_dihedral_angle_d16.7451213
X-RAY DIFFRACTIONf_chiral_restr0.068492
X-RAY DIFFRACTIONf_plane_restr0.005570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4135-2.52330.38311170.29252127X-RAY DIFFRACTION77
2.5233-2.65620.27671340.25922508X-RAY DIFFRACTION90
2.6562-2.82240.3251390.24712651X-RAY DIFFRACTION94
2.8224-3.040.30461390.23422683X-RAY DIFFRACTION96
3.04-3.34530.25651460.21042784X-RAY DIFFRACTION99
3.3453-3.82790.28481480.20022817X-RAY DIFFRACTION100
3.8279-4.81720.19991510.16562837X-RAY DIFFRACTION100
4.8172-25.1890.20951560.17872946X-RAY DIFFRACTION99
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)
12.11990.0679-0.98211.2452-1.37971.6499-0.01230.49750.4592-0.0404-0.0345-0.0716-0.71920.0115-0.15080.3794-0.0329-0.06180.24030.10180.372-38.7685-18.8382-36.4261
21.7564-0.3355-0.15151.1121-0.54393.3956-0.10620.19010.0504-0.0057-0.0808-0.0812-0.13730.29990.08290.2421-0.063-0.02150.28170.06380.2246-35.5088-26.9628-33.8521
33.4999-1.0133-0.93650.9046-0.0630.41970.07340.91971.2966-0.06430.0291-0.113-0.3485-0.0771-0.02330.42240.0164-0.06290.34580.05170.6586-24.3405-10.103911.3912
42.71331.52350.08710.86610.26384.0804-0.3910.37011.08220.3715-0.31020.3464-1.27350.38680.151.25510.0629-0.04880.85110.47271.0863-19.9357-6.52565.9219
52.4997-0.80110.27431.26520.33410.4244-0.1098-0.11770.05090.48490.0767-0.15930.3338-0.08750.00670.446-0.0087-0.08440.3843-0.07460.3225-25.2494-18.719518.4927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:73)
2X-RAY DIFFRACTION2(chain A and resid 74:231)
3X-RAY DIFFRACTION3(chain A and resid 232:1102)
4X-RAY DIFFRACTION4(chain A and resid 1103:1113)
5X-RAY DIFFRACTION5(chain A and resid 1129:1216)

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