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- PDB-1p28: The crystal structure of a pheromone binding protein from the coc... -

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Basic information

Entry
Database: PDB / ID: 1p28
TitleThe crystal structure of a pheromone binding protein from the cockroach Leucophaea maderae in complex with a component of the pheromonal blend: 3-hydroxy-butan-2-one.
Componentspheromone binding proteinInsect pheromone-binding protein
KeywordsTRANSPORT PROTEIN / Pheromone binding protein / 3-hydroxy-butan-2-one
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
R,3-HYDROXYBUTAN-2-ONE / S,3-HYDROXYBUTAN-2-ONE / Pheromone binding protein
Similarity search - Component
Biological speciesLeucophaea maderae (Madeira cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
DepositionApr 15, 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

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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)28,6706
Polymers28,3182
Non-polymers3524
Water4,252236
1
A: pheromone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3353
Polymers14,1591
Non-polymers1762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: pheromone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3353
Polymers14,1591
Non-polymers1762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.217, 62.210, 45.117
Angle α, β, γ (deg.)90.00, 92.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein pheromone binding protein / Insect 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) / 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-HBS / S,3-HYDROXYBUTAN-2-ONE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-HBR / R,3-HYDROXYBUTAN-2-ONE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 1.89 Å3/Da / Density % sol: 34.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: NaCitrate, Na/K Tartrate, Ammonium Sulfate, pH 5.6, 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: 0.919214 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 4, 2002 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919214 Å / Relative weight: 1
ReflectionResolution: 1.7→29.748 Å / Num. all: 23078 / Num. obs: 23078 / % possible obs: 97 % / Redundancy: 3.5 % / Rsym value: 0.046 / Net I/σ(I): 10.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.182 / % possible all: 93.1
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / % possible obs: 97 % / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 93.1 % / Rmerge(I) obs: 0.182

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.865 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18447 1904 8.4 %RANDOM
Rwork0.14135 ---
all0.14508 23380 --
obs0.14508 20755 96.92 %-
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: 15.895 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.18 Å2
2--0.74 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1799 0 24 236 2059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221857
X-RAY DIFFRACTIONr_bond_other_d0.0020.021652
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9842510
X-RAY DIFFRACTIONr_angle_other_deg1.67133861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2825234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022084
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02348
X-RAY DIFFRACTIONr_nbd_refined0.2190.2480
X-RAY DIFFRACTIONr_nbd_other0.2450.21965
X-RAY DIFFRACTIONr_nbtor_other0.0880.21080
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2810.2145
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0920.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.320.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8711.51176
X-RAY DIFFRACTIONr_mcangle_it1.5621890
X-RAY DIFFRACTIONr_scbond_it2.3633681
X-RAY DIFFRACTIONr_scangle_it3.8754.5620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.21 133
Rwork0.168 1485
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)
10.4056-0.2334-0.18070.8090.07690.60960.03210.00960.00030.0521-0.0357-0.0522-0.02150.01620.00360.0094-0.0058-0.00370.010.00560.03846.8070.2162.519
20.59880.2241-0.96670.7179-0.53011.4373-0.03920.02140.00390.0346-0.0204-0.03740.01080.00620.05970.011-0.0052-0.01190.0124-0.00120.01757.57522.72520.153
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 11710 - 128
2X-RAY DIFFRACTION2BB3 - 11814 - 129
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.141 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5
LS refinement shell
*PLUS
Highest resolution: 1.7 Å

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