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- PDB-1ow4: Crystal structure of a pheromone binding protein from the cockroa... -

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Basic information

Entry
Database: PDB / ID: 1ow4
TitleCrystal structure of a pheromone binding protein from the cockroach Leucophaea maderae in complex with the fluorescent reporter ANS (1-anilinonaphtalene-8-sulfonic acid),
Componentspheromone binding protein
KeywordsTRANSPORT PROTEIN / Pheromone Binding Protein / ligand 8-anilino-1-naphtalenesulfonic acid
Function / homology
Function and homology information


Pheromone/general odorant binding protein domain / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
8-ANILINO-1-NAPHTHALENE SULFONATE / Pheromone binding protein
Similarity search - Component
Biological speciesLeucophaea maderae (Madeira cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLartigue, A. / Gruez, A. / Spinelli, S. / Riviere, S. / Brossut, R. / Tegoni, M. / Cambillau, C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: THE CRYSTAL STRUCTURE OF A COCKROACH PHEROMONE-BINDING PROTEIN SUGGESTS A NEW LIGAND BINDING AND RELEASE MECHANISM
Authors: Lartigue, A. / Gruez, A. / Spinelli, S. / Riviere, S. / Brossut, R. / Tegoni, M. / Cambillau, C.
History
DepositionMar 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 3, 2024Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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: pheromone binding protein
B: pheromone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1016
Polymers28,3182
Non-polymers7834
Water4,378243
1
A: pheromone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5503
Polymers14,1591
Non-polymers3912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: pheromone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5503
Polymers14,1591
Non-polymers3912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.422, 45.070, 45.379
Angle α, β, γ (deg.)118.55, 92.63, 107.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein pheromone binding protein


Mass: 14159.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leucophaea maderae (Madeira cockroach) / Gene: Pheromone Binding Protein (PBP) / Plasmid: pET22b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q8MTC1
#2: Chemical ChemComp-2AN / 8-ANILINO-1-NAPHTHALENE SULFONATE


Mass: 299.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13NO3S
#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.: 243 / 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: 2.6 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: PEG 10000, Imidazole/malate., pH 8.5, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Method: unknown / Details: Sulzenbacher, G., (2002) Acta Cryst., D58, 2109.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97887 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2002 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 1.6→25.906 Å / Num. all: 34113 / Num. obs: 31333 / % possible obs: 84.4 % / Observed criterion σ(F): 4.8 / Redundancy: 1.9 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 7.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 4.8 / Rsym value: 0.122 / % possible all: 84.4
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 84 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Lma-PBP (native)

Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.633 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 4.8 / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20843 1565 5 %RANDOM
Rwork0.17433 ---
all0.176 37118 --
obs0.17602 29762 84.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.02 Å2-0.89 Å2
2--0.47 Å20.21 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 54 243 2118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221931
X-RAY DIFFRACTIONr_bond_other_d0.0040.021683
X-RAY DIFFRACTIONr_angle_refined_deg1.7622.0062611
X-RAY DIFFRACTIONr_angle_other_deg2.85333943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8725237
X-RAY DIFFRACTIONr_chiral_restr0.1010.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022143
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02382
X-RAY DIFFRACTIONr_nbd_refined0.2160.2509
X-RAY DIFFRACTIONr_nbd_other0.2480.22153
X-RAY DIFFRACTIONr_nbtor_other0.1010.21139
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.360.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.218
X-RAY DIFFRACTIONr_mcbond_it0.8991.51195
X-RAY DIFFRACTIONr_mcangle_it1.63521927
X-RAY DIFFRACTIONr_scbond_it2.5643736
X-RAY DIFFRACTIONr_scangle_it3.9454.5684
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 82
Rwork0.183 1355
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)
11.603-0.01210.52370.6511-0.2730.84330.0264-0.0568-0.0389-0.0036-0.0419-0.01540.0009-0.05450.01550.0314-0.00590.02470.03-0.01030.0388-14.50410.923-10.406
21.44730.020.50651.1453-0.08490.7601-0.01290.0779-0.0008-0.0318-0.0014-0.03980.01580.07480.01430.0230.00080.02760.0352-0.00310.03364.875-10.8128.574
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 11811 - 129
2X-RAY DIFFRACTION2BB0 - 11811 - 129
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.174 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.76
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.64 Å

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