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- PDB-2qev: Crystal Structure of Anopheles gambiae D7r4 -

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Basic information

Entry
Database: PDB / ID: 2qev
TitleCrystal Structure of Anopheles gambiae D7r4
ComponentsD7R4 Protein
KeywordsLIGAND BINDING PROTEIN / All-helical / Odorant-binding protein
Function / homologyPheromone/general odorant binding protein domain / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha / Short form salivary protein D7R4
Function and homology information
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.998 Å
AuthorsAndersen, J.F. / Mans, B.J. / Calvo, E. / Ribeiro, J.M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Crystal Structure of D7r4, a Salivary Biogenic Amine-binding Protein from the Malaria Mosquito Anopheles gambiae
Authors: Mans, B.J. / Calvo, E. / Ribeiro, J.M. / Andersen, J.F.
History
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D7R4 Protein


Theoretical massNumber of molelcules
Total (without water)17,1001
Polymers17,1001
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.651, 62.651, 42.773
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein D7R4 Protein / D7-related 4 protein


Mass: 17099.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Strain: G3 / Gene: D7r4 / Plasmid: pET17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9BIH3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20 % PEG 6000, 0.1 M Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791533 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2005 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791533 Å / Relative weight: 1
Reflection

D res high: 2.5 Å / D res low: 30 Å / % possible obs: 99.9

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs
317.8345780.0390.4511430
4.926.6561720.0710.7611400
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.383099.310.0260.5442.9
4.275.3810010.0280.4813
3.734.2799.910.030.443.1
3.393.7310010.0360.4323.1
3.153.3910010.050.5653.1
2.963.1510010.0670.3633.1
2.822.9610010.1090.3653.1
2.692.8210010.1660.5753.1
2.592.6910010.1920.3563
2.52.5999.810.2590.3862.9
5.383099.520.0391.0164.8
4.275.3810020.0491.1515
3.734.2710020.0591.1075
3.393.7310020.0771.0035.1
3.153.3910020.1030.7555.1
2.963.1510020.1360.5945.1
2.822.9610020.2280.4885.1
2.692.8210020.3380.5475
2.592.6910020.3960.4314.9
2.52.5999.220.5460.5194.3
ReflectionResolution: 1.998→62.62 Å / Num. all: 11190 / Num. obs: 11190 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.039 / Χ2: 1.341 / Net I/σ(I): 18.3
Reflection shellResolution: 1.998→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 3.3 / Num. unique all: 941 / Χ2: 0.905 / % possible all: 84.3

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.49 Å / D res low: 50 Å / FOM : 0.4 / FOM acentric: 0.408 / FOM centric: 0.31 / Reflection: 5940 / Reflection acentric: 5448 / Reflection centric: 492
Phasing MAD set

Highest resolution: 2.49 Å / Lowest resolution: 50 Å / Reflection centric: 492

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentric
11.67100005448
20.810.743.44.81.020.895445
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
114.77-501.0110.20.1001610
18.67-14.770.9810.20.1009528
16.13-8.671.9610.20.10022641
14.74-6.131.4910.10.10041455
13.87-4.741.2210.100067569
13.27-3.871.461000096281
12.83-3.277.1210000133699
12.49-2.832.69100001724109
214.77-500.520.76.89.71.991.91610
28.67-14.770.610.5468.52.41.729528
26.13-8.670.530.474.44.52.522.1822641
24.74-6.130.610.634.56.21.851.0741455
23.87-4.740.780.794.75.81.140.7167569
23.27-3.870.860.9144.90.850.5396281
22.83-3.270.930.9833.60.650.39133599
22.49-2.830.991.012.330.460.31722109
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se65.355190.7350.5960.0480
2Se61.072320.8850.6770.2740
3Se141.814610.7630.5620.3380
4Se83.9570.8830.8160.0940
5Se59.452150.7350.5970.0570.157
6Se72.061380.8860.6770.2770.149
7Se117.020420.7630.5630.3410.164
8Se84.492190.8830.8190.0930.12
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
14.77-500.7810.8080.737261610
8.67-14.770.8050.8280.7231239528
6.13-8.670.8180.8510.63426722641
4.74-6.130.7730.7970.59946941455
3.87-4.740.6340.6580.39674467569
3.27-3.870.4920.5120.263104396281
2.83-3.270.310.3240.1251435133699
2.49-2.830.1340.140.04718331724109
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 5940
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.77-10047.70.887501
4.56-5.7738.90.927506
3.96-4.5647.20.903505
3.59-3.9646.20.902504
3.33-3.5950.30.888502
3.13-3.3354.30.864502
2.98-3.1353.40.886503
2.84-2.9860.20.869515
2.73-2.8468.70.856502
2.64-2.7372.50.827512
2.49-2.6476.80.799888

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT2data extraction
EPICS-baseddata aquisition systemdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.998→62.62 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.1 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.213 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 533 4.8 %RANDOM
Rwork0.219 ---
obs0.22 11190 98.15 %-
all-11190 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.093 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.53 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.998→62.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1189 0 0 72 1261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221215
X-RAY DIFFRACTIONr_angle_refined_deg1.061.9771634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3722460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94215237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.589159
X-RAY DIFFRACTIONr_chiral_restr0.0950.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02908
X-RAY DIFFRACTIONr_nbd_refined0.2590.3591
X-RAY DIFFRACTIONr_nbtor_refined0.3210.5849
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.5104
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.323
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.57
X-RAY DIFFRACTIONr_mcbond_it3.9191.5740
X-RAY DIFFRACTIONr_mcangle_it5.00621175
X-RAY DIFFRACTIONr_scbond_it7.0953518
X-RAY DIFFRACTIONr_scangle_it9.8334.5459
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 31 -
Rwork0.317 695 -
obs-726 85.82 %
Refinement TLS params.Method: refined / Origin x: 8.3779 Å / Origin y: -22.4167 Å / Origin z: 0.7442 Å
111213212223313233
T-0.0441 Å20.0299 Å2-0.0256 Å2-0.0604 Å2-0.072 Å2---0.033 Å2
L1.853 °20.0847 °21.1752 °2-0.5588 °20.3301 °2--1.714 °2
S-0.2977 Å °-0.0943 Å °0.2868 Å °-0.0688 Å °0.1145 Å °-0.0708 Å °-0.2412 Å °-0.2394 Å °0.1832 Å °

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