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- PDB-4run: Crystal structure of human odorant binding protein OBPIIa -

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Basic information

Entry
Database: PDB / ID: 4run
TitleCrystal structure of human odorant binding protein OBPIIa
ComponentsOdorant-binding protein 2a
KeywordsTRANSPORT PROTEIN / human lipocalin / lipid binding protein / odorant binding protein / vanillin / lilial / fatty acids / aliphatic aldehydes / nasal mucus
Function / homology
Function and homology information


sensory perception of chemical stimulus / odorant binding / response to stimulus / small molecule binding / sensory perception of smell / extracellular region
Similarity search - Function
von Ebner's gland protein/ Bos/Can allergen / Lipocalin / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / Odorant-binding protein 2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSchiefner, A. / Skerra, A.
CitationJournal: Proteins / Year: 2015
Title: Crystal structure of the human odorant binding protein, OBPIIa.
Authors: Schiefner, A. / Freier, R. / Eichinger, A. / Skerra, A.
History
DepositionNov 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Odorant-binding protein 2a
B: Odorant-binding protein 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5003
Polymers37,3112
Non-polymers1891
Water27015
1
A: Odorant-binding protein 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8442
Polymers18,6551
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Odorant-binding protein 2a


Theoretical massNumber of molelcules
Total (without water)18,6551
Polymers18,6551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-7 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.949, 52.949, 232.098
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 8 - 152 / Label seq-ID: 8 - 152

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Odorant-binding protein 2a / Odorant-binding protein IIa / OBPIIa


Mass: 18655.281 Da / Num. of mol.: 2 / Mutation: C99S, K112N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OBP2A / Plasmid: pASK75-his / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: Q9NY56
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: Protein solution: 14 mg/ml protein, 0.2 M imidazole, 0.4 M NaCl, 10 mM Tris-HCl, 1.3 mM Menthol, 3.3 %(v/v) Methanol; Reservoir solution: 20 %(w/v) PEG 3350, 0.1 M ammonium citrate, pH 3.5, ...Details: Protein solution: 14 mg/ml protein, 0.2 M imidazole, 0.4 M NaCl, 10 mM Tris-HCl, 1.3 mM Menthol, 3.3 %(v/v) Methanol; Reservoir solution: 20 %(w/v) PEG 3350, 0.1 M ammonium citrate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2011 / Details: MIRRORS
RadiationMonochromator: SI-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→35 Å / Num. all: 10926 / Num. obs: 10926 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 63.91 Å2 / Rmerge(I) obs: 0.049 / Χ2: 0.985 / Net I/σ(I): 31.88
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.6-2.70.6452.7672941113197.5
2.7-2.80.4325.068593978199.9
2.8-30.2977.571505715851100
3-3.20.16113.811166012281100
3.2-3.50.08126.041289813691100
3.5-40.0541.511362114671100
4-50.0364.581352214991100
5-60.02865.7859366781100
6-80.02766.1747105561100
8-100.01880.6917052131100
10-350.016811695240196.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
MAR345data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EYC

3eyc


Resolution: 2.6→33.7 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.866 / WRfactor Rfree: 0.2651 / WRfactor Rwork: 0.2213 / FOM work R set: 0.7801 / SU B: 33.044 / SU ML: 0.328 / SU R Cruickshank DPI: 1.1842 / SU Rfree: 0.3639 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.184 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 523 4.8 %RANDOM
Rwork0.235 ---
all0.2373 10926 --
obs0.2373 10926 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 174.07 Å2 / Biso mean: 75.6 Å2 / Biso min: 36.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20 Å2
2---0.92 Å20 Å2
3---1.83 Å2
Refinement stepCycle: LAST / Resolution: 2.6→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 13 15 2433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192464
X-RAY DIFFRACTIONr_bond_other_d0.0030.022378
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9883309
X-RAY DIFFRACTIONr_angle_other_deg0.90835490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55323.644118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35415465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7011522
X-RAY DIFFRACTIONr_chiral_restr0.070.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212744
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02554
X-RAY DIFFRACTIONr_mcbond_it2.163.9821194
X-RAY DIFFRACTIONr_mcbond_other2.163.9811193
X-RAY DIFFRACTIONr_mcangle_it3.747.4561489
Refine LS restraints NCS

Ens-ID: 1 / Number: 7513 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 36 -
Rwork0.348 728 -
all-764 -
obs--97.2 %
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)
13.81260.964-2.0124.0618-2.06045.3728-0.0285-0.5280.13430.2079-0.148-0.6644-0.13370.71220.17650.27950.01280.00070.2162-0.02570.1396-19.193123.8611-16.101
22.60610.86770.61326.58231.29513.47430.0953-0.9588-0.19520.9495-0.0045-0.17780.20640.0078-0.09090.39860.0195-0.03220.38660.04910.0477-34.8588-2.0193-12.5376
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 154
2X-RAY DIFFRACTION2B2 - 153

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