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- PDB-1org: The crystal structure of a pheromone binding protein from the coc... -

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Basic information

Entry
Database: PDB / ID: 1org
TitleThe crystal structure of a pheromone binding protein from the cockroach Leucophaea maderae reveals a new mechanism of pheromone binding
Componentspheromone binding protein
KeywordsTRANSPORT PROTEIN / Pheromone binding Protein / APO-FORM / 6 ALPHA HELIX
Function / homologyPheromone/general odorant binding protein domain / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha / Pheromone binding protein
Function and homology information
Biological speciesLeucophaea maderae (Madeira cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 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 13, 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 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pheromone binding protein
B: pheromone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2144
Polymers26,0302
Non-polymers1842
Water3,369187
1
A: pheromone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1072
Polymers13,0151
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: pheromone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1072
Polymers13,0151
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.303, 44.930, 45.562
Angle α, β, γ (deg.)118.13, 93.18, 107.15
Int Tables number1
Space group name H-MP1

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Components

#1: Protein pheromone binding protein


Mass: 13014.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leucophaea maderae (Madeira cockroach) / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.58 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: Tris, PEG 2000, pH 8.0, 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: BM14 / Wavelength: 0.97887 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 23, 2002 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. all: 29653 / Num. obs: 29653 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.045 / Net I/σ(I): 8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.045 / Mean I/σ(I) obs: 2.4 / % possible all: 94.8
Reflection
*PLUS
% possible obs: 95.7 % / Redundancy: 6 %
Reflection shell
*PLUS
% possible obs: 94.8 % / Rmerge(I) obs: 0.274

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.027 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2.4 / ESU R: 0.106 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21366 2971 10 %RANDOM
Rwork0.18073 ---
all0.184 29000 --
obs0.18404 26680 95.77 %-
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: 24.378 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0.56 Å2-1.57 Å2
2--0.38 Å20.12 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 12 187 2002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221842
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9762491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7755234
X-RAY DIFFRACTIONr_chiral_restr0.0840.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021392
X-RAY DIFFRACTIONr_nbd_refined0.2190.2935
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.29
X-RAY DIFFRACTIONr_mcbond_it0.7211.51175
X-RAY DIFFRACTIONr_mcangle_it1.27721890
X-RAY DIFFRACTIONr_scbond_it2.3373667
X-RAY DIFFRACTIONr_scangle_it3.5494.5601
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.255 215
Rwork0.223 1957
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)
11.92650.11850.27241.7265-0.2891.61250.0537-0.0689-0.08530.1156-0.0644-0.10530.0541-0.02750.01070.052-0.00990.01140.0495-0.01360.0314-14.37810.844-10.409
21.63760.38870.51752.2792-0.01091.7519-0.0420.10050.0573-0.06130.04830.03880.03990.035-0.00630.01740.01330.0230.0540.00150.03634.69-10.6688.694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1181 - 118
2X-RAY DIFFRACTION2BB1 - 1181 - 118
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.181 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.43
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.74 Å

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