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- PDB-4c41: Corticosteroid-binding globulin with engineered disulphide bridge... -

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Basic information

Entry
Database: PDB / ID: 4c41
TitleCorticosteroid-binding globulin with engineered disulphide bridge between residues 100 and 236
ComponentsCORTICOSTEROID-BINDING GLOBULIN
KeywordsTRANSPORT PROTEIN / SERPIN / ENGINEERED DISULPHIDE
Function / homology
Function and homology information


Glucocorticoid biosynthesis / glucocorticoid metabolic process / Prednisone ADME / steroid binding / serine-type endopeptidase inhibitor activity / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Corticosteroid-binding globulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChan, W.L. / Zhou, A. / Read, R.J.
CitationJournal: Plos One / Year: 2014
Title: Towards Engineering Hormone-Binding Globulins as Drug Delivery Agents.
Authors: Chan, W.L. / Zhou, A. / Read, R.J.
History
DepositionAug 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CORTICOSTEROID-BINDING GLOBULIN


Theoretical massNumber of molelcules
Total (without water)41,6461
Polymers41,6461
Non-polymers00
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.130, 73.390, 126.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CORTICOSTEROID-BINDING GLOBULIN / CBG / SERPIN A6 / TRANSCORTIN


Mass: 41645.504 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-405 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Plasmid: PSUMO 3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P08185
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE OF OUR PROTEIN DIFFERS FROM WILD TYPE BY 3 MUTATIONS (S100C, V236C, T361R).

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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: 2.36 Å3/Da / Density % sol: 47.86 % / Description: NONE
Crystal growpH: 5.3 / Details: 15% PEG3350, 0.2M NACL, 50MM MES, PH 5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→39.98 Å / Num. obs: 31617 / % possible obs: 84.7 % / Observed criterion σ(I): 2.5 / Redundancy: 8.2 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.47
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.71 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1702)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VDY

2vdy


Resolution: 1.8→39.977 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2064 1570 5 %
Rwork0.176 --
obs0.1775 31460 84.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→39.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2820 0 0 295 3115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032998
X-RAY DIFFRACTIONf_angle_d0.8034090
X-RAY DIFFRACTIONf_dihedral_angle_d12.6881070
X-RAY DIFFRACTIONf_chiral_restr0.032480
X-RAY DIFFRACTIONf_plane_restr0.003523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85810.26361530.25673078X-RAY DIFFRACTION97
1.8581-1.92450.25491010.23831935X-RAY DIFFRACTION70
1.9245-2.00160.2693930.21282044X-RAY DIFFRACTION74
2.0016-2.09270.24181420.19782540X-RAY DIFFRACTION81
2.0927-2.2030.19461710.18553092X-RAY DIFFRACTION97
2.203-2.3410.23441240.18182540X-RAY DIFFRACTION79
2.341-2.52170.21371600.17743008X-RAY DIFFRACTION95
2.5217-2.77540.20141550.17712866X-RAY DIFFRACTION89
2.7754-3.17690.18371630.17433060X-RAY DIFFRACTION94
3.1769-4.0020.2011450.16082639X-RAY DIFFRACTION81
4.002-39.98730.18231630.14443088X-RAY DIFFRACTION90
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)
10.58540.0614-0.42031.04570.15641.99030.0111-0.0627-0.02270.0966-0.0265-0.03490.06880.0890.02170.0831-0.0005-0.00790.1010.00310.132317.8756-3.5977-19.9951
20.8722-0.1710.35890.9324-0.44551.76430.0293-0.1330.15040.17140.0170.1468-0.1567-0.2376-0.05760.14140.00720.03980.1594-0.02530.1733.98324.8094-11.9165
33.59660.4403-1.51360.916-0.33932.20420.01870.16610.1873-0.04370.09680.2437-0.0172-0.2698-0.12050.11350.0009-0.01830.09550.00710.14045.69474.763-24.5224
41.559-0.10210.57533.1912-0.0262.1565-0.02720.082-0.0412-0.1303-0.0175-0.06310.12390.07570.05050.097-0.00820.03580.10760.00370.083524.18272.3708-46.2794
56.24191.7508-0.5954.7190.18494.99960.2013-0.1433-0.1103-0.2115-0.2253-0.32060.46340.2233-0.01310.14230.07050.02130.08370.01330.170828.0302-10.6348-38.0243
60.86870.4573-1.14790.734-0.79723.0397-0.10310.002-0.0808-0.06250.0174-0.00590.294-0.15030.09950.0976-0.0089-0.01430.1053-0.00550.130912.9428-5.9717-26.672
72.77952.7307-3.48753.129-3.77395.07820.02070.03830.04550.05870.03330.0927-0.0292-0.2634-0.06130.0996-0.0095-0.00270.1299-0.00630.11798.57410.7869-27.0911
80.89780.1628-1.26741.189-0.8335.3033-0.00560.013-0.0282-0.05320.0219-0.03760.03490.1136-0.01590.07540.0195-0.00130.062-0.00310.121821.2446-1.4594-38.4804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 15 THROUGH 112 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 113 THROUGH 155 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 156 THROUGH 184 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 185 THROUGH 246 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 247 THROUGH 269 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 270 THROUGH 317 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 318 THROUGH 348 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 349 THROUGH 383 )

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