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- PDB-4kii: Beta-lactoglobulin in complex with Cp*Rh(III)Cl N,N-di(pyridin-2-... -

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Basic information

Entry
Database: PDB / ID: 4kii
TitleBeta-lactoglobulin in complex with Cp*Rh(III)Cl N,N-di(pyridin-2-yl)dodecanamide
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / beta-barrel / fatty acid binding / milk / artificial metalloenzyme
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
[N,N-di(pyridin-2-yl-kappaN)dodecanamide]rhodium / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsCherrier, M.V. / Amara, P. / Engilberge, S. / Fontecilla-Camps, J.C.
CitationJournal: Eur.J.Inorg.Chem. / Year: 2013
Title: Structural Basis for Enantioselectivity in the Transfer Hydrogenation of a Ketone Catalyzed by an Artificial Metalloenzyme
Authors: Cherrier, M.V. / Amara, P. / Engilberge, S. / Chevalley, A. / Salmain, M. / Fontecilla-Camps, J.C.
History
DepositionMay 2, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8442
Polymers18,3871
Non-polymers4561
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.950, 52.950, 110.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18387.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02754
#2: Chemical ChemComp-RHL / [N,N-di(pyridin-2-yl-kappaN)dodecanamide]rhodium


Mass: 456.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H31N3ORh
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE HAS NATURAL VARIANTS(80, 134).

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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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.44 M trisodium citrate 100 mM Tris HCl pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97908 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2012 / Details: mirrors
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.85→45.856 Å / Num. obs: 15842 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Biso Wilson estimate: 46.049 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 30.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.85-1.950.9620.4386.1323081229422630.46198.6
1.95-2.050.990.21511.1318098185518310.22798.7
2.05-2.150.9930.1415.1814130153415230.14899.3
2.15-2.250.9970.10221.1112910127512610.10798.9
2.25-2.50.9980.07227.1723765237823600.07699.2
2.5-30.9990.04439.0625800272427110.04699.5
3-40.9990.03154.0219878220822030.03399.8
4-60.9990.02866.3210526116311560.02999.4
6-100.9990.02768.432414104040.02998.5
1010.02967.7510191301300.031100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.65 Å45.86 Å
Translation5.65 Å45.86 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NPO

3npo


Resolution: 1.85→45.856 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.22 / σ(F): 2.01 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 1579 9.97 %Random
Rwork0.1874 ---
obs0.1907 15841 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.8 Å2 / Biso mean: 49.7151 Å2 / Biso min: 23.08 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1242 0 27 92 1361
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_deg1.199
X-RAY DIFFRACTIONf_dihedral_angle_d15.806
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)
12.60470.39690.22112.6358-2.41792.291-0.25970.37870.3185-0.31380.05830.00720.08860.12820.1980.518-0.08630.11710.3346-0.02960.487549.502640.2816107.5992
21.7609-0.18320.73154.3533-0.4874.1804-0.1532-0.11490.1298-0.2130.23760.2735-0.3971-0.7232-0.04230.37210.04530.01340.30490.05080.348735.435744.728121.9642
33.21730.3584-0.37113.2744-1.63555.8792-0.59410.9381-0.0572-0.92850.35790.24050.8339-0.49820.15140.5615-0.1528-0.0590.4599-0.05720.378938.783635.5757105.0091
43.6881-0.7534-4.89816.132-0.78588.1303-0.30091.8185-1.0945-0.20160.11.1567-0.4308-2.7168-0.09180.4113-0.0544-0.05150.70020.02860.550628.892238.1143114.0269
59.70046.2142-6.81687.1789-4.83925.0243-0.08740.2210.3714-0.90680.62280.81230.8915-0.4813-0.52420.4336-0.1282-0.14620.56960.1290.502132.793239.8153106.2625
66.69891.7909-2.05454.61280.26524.57910.01830.93081.3358-0.21920.24180.9329-0.652-1.7349-0.42280.5218-0.0175-0.03490.65910.1480.466340.396750.163102.8091
75.42230.2258-2.62455.8883-0.22657.0257-0.1620.0807-0.10250.1938-0.1064-0.2818-0.0166-0.14910.22260.2914-0.07860.01550.2209-0.00890.27547.577941.9481111.526
86.11465.10490.1425.9487-1.10831.5308-0.2750.27060.823-0.173-0.7848-1.1626-1.17550.6597-0.87940.94570.1822-0.07010.79730.18660.687939.642157.3111114.1945
91.65660.0196-1.17752.30140.53854.611-0.0788-0.0725-0.0999-0.48310.0481-1.06680.3430.2540.07640.3523-0.01580.00530.2182-0.01940.338944.913936.5835118.5492
103.2717-0.64480.34494.34720.08384.31780.3079-0.58060.17430.3231-0.3757-1.9561-0.11860.7424-0.08870.4268-0.1256-0.09910.46060.03140.635552.652642.0183122.5019
111.6685-1.2611.05573.42260.79331.6134-0.2377-0.33790.371.34040.0606-1.2446-0.45150.33930.2110.5398-0.0731-0.02560.2688-0.03590.400742.862245.7721125.1546
126.832-3.28161.76597.971-0.57646.5596-0.0311-0.1117-0.59110.40960.13711.33990.9883-1.2811-0.18580.4027-0.14950.10060.3562-0.020.424234.834430.4582123.5946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 2 through 19 )A0
2X-RAY DIFFRACTION2chain A and (resid 20 through 41 )A0
3X-RAY DIFFRACTION3chain A and (resid 42 through 53 )A0
4X-RAY DIFFRACTION4chain A and (resid 54 through 65 )A0
5X-RAY DIFFRACTION5chain A and (resid 66 through 75 )A0
6X-RAY DIFFRACTION6chain A and (resid 76 through 89 )A0
7X-RAY DIFFRACTION7chain A and (resid 90 through 108 )A0
8X-RAY DIFFRACTION8chain A and (resid 109 through 116 )A0
9X-RAY DIFFRACTION9chain A and (resid 117 through 129 )A0
10X-RAY DIFFRACTION10chain A and (resid 130 through 141 )A0
11X-RAY DIFFRACTION11chain A and (resid 142 through 152 )A0
12X-RAY DIFFRACTION12chain A and (resid 153 through 162 )A0

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