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- PDB-4n7c: Structural re-examination of native Bla g 4 -

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Basic information

Entry
Database: PDB / ID: 4n7c
TitleStructural re-examination of native Bla g 4
ComponentsBla g 4 allergen variant 1
KeywordsPROTEIN BINDING / Allergen / Beta barrel / 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
4-(2-aminoethyl)phenol / CITRIC ACID / Bla g 4 allergen variant 1
Similarity search - Component
Biological speciesBlattella germanica (German cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _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 1.3Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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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)20,8895
Polymers20,3761
Non-polymers5134
Water2,288127
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)41,77810
Polymers40,7522
Non-polymers1,0278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3750 Å2
ΔGint-17 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.354, 60.354, 125.409
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-

MET

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Components

#1: Protein Bla g 4 allergen variant 1


Mass: 20375.754 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-AEF / 4-(2-aminoethyl)phenol


Mass: 137.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.8 Å3/Da / Density % sol: 56.11 %
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: 1.75→50 Å / Num. all: 45386 / Num. obs: 45386 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 43.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.75 / Rsym value: 0.5 / % 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: 1.75→34.39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.78 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21346 1229 5.1 %RANDOM
Rwork0.18569 ---
obs0.1871 22948 99.93 %-
all-22948 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å20 Å2
2--0.15 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.75→34.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 35 127 1532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191475
X-RAY DIFFRACTIONr_bond_other_d00.021296
X-RAY DIFFRACTIONr_angle_refined_deg2.2331.9542003
X-RAY DIFFRACTIONr_angle_other_deg3.8533.0062955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7585178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18823.675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63615219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6271510
X-RAY DIFFRACTIONr_chiral_restr0.1290.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021707
X-RAY DIFFRACTIONr_gen_planes_other0.0310.02369
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 99 -
Rwork0.285 1654 -
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)
12.7245-0.62570.16145.6751-2.46166.0305-0.0619-0.3543-0.01150.278-0.1509-0.661-0.1420.7040.21290.0737-0.0191-0.07310.14380.04120.192133.2916.774417.291
21.23070.4073-0.40663.3033-0.61520.9054-0.0442-0.02910.0217-0.15640.0070.0518-0.0060.03140.03720.1956-0.009-0.04320.01930.00690.066417.82446.703311.7261
32.5515-1.0730.39563.78420.70211.7413-0.0291-0.37350.02570.0815-0.0890.2682-0.1235-0.03640.11810.22690.0054-0.03660.09250.01260.132715.54589.330116.0426
40.27340.61790.99789.22360.56164.82160.0048-0.09750.11360.5080.04090.277-0.1988-0.1636-0.04570.1982-0.01520.01650.1307-0.17130.319917.226511.488521.8968
51.26270.10130.0862.4536-0.63941.4948-0.1118-0.0957-0.0085-0.0499-0.0156-0.26190.07440.21050.12750.1444-0.0003-0.02220.05220.01820.067525.00682.692215.1875
64.2969-0.68192.70761.453-1.6664.7155-0.16670.30430.1907-0.1235-0.0142-0.150.1065-0.09630.18090.2026-0.03190.01410.0845-0.00090.067817.06516.1310.653
79.4465-1.1366-0.82477.2598-2.31218.3267-0.25980.494-0.4422-0.56930.64320.64010.7441-1.2801-0.38340.2653-0.1965-0.05410.2970.05710.081711.6451-1.1824-0.3144
82.36651.1298-0.05523.9601-1.33830.8997-0.2520.0776-0.4071-0.38680.0171-0.52320.35440.10480.23490.28310.02940.07370.0765-0.00430.196826.6389-6.97456.7852
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 - 174

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