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- PDB-2v95: Structure of Corticosteroid-Binding Globulin in complex with Cortisol -

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Basic information

Entry
Database: PDB / ID: 2v95
TitleStructure of Corticosteroid-Binding Globulin in complex with Cortisol
ComponentsCORTICOSTEROID-BINDING GLOBULIN
KeywordsTRANSPORT PROTEIN / CBG / RCL / SERPIN / SECRETED / TRANSPORT / GLYCOPROTEIN / LIPID-BINDING / GLUCOCORTICOIDS / STEROID-BINDING / STEROID TRANSPORTER / CORTICOSTEROID-BINDING GLOBULIN TRANSPORT PROTEIN
Function / homology
Function and homology information


Glucocorticoid biosynthesis / glucocorticoid metabolic process / negative regulation of endopeptidase activity / steroid binding / serine-type endopeptidase inhibitor activity / extracellular space
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
Chem-HCY / Corticosteroid-binding globulin
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsKlieber, M.A. / Muller, Y.A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Corticosteroid-Binding Globulin: Structural Basis for Steroid Transport and Proteinase-Triggered Release
Authors: Klieber, M.A. / Underhill, C. / Hammond, G.L. / Muller, Y.A.
History
DepositionAug 21, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionSep 4, 2007ID: 2V6D
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CORTICOSTEROID-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2522
Polymers41,8891
Non-polymers3621
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)122.110, 54.250, 61.040
Angle α, β, γ (deg.)90.00, 97.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 41889.457 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-396 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: LIVER / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K12 BL21(DE3)STAR / References: UniProt: P31211
#2: Chemical ChemComp-HCY / (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione / CORTISOL


Mass: 362.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O5 / Comment: medication, hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 163 TO ASN ENGINEERED RESIDUE IN CHAIN A, ARG 164 TO GLN
Sequence detailsAMINO ACIDS 163 AND 164 TR REPLACED BY NQ

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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: 2.37 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 8.5
Details: 1 MICROLITER OF 15 MG/ML RECOMBINANT RAT CBG AND 1 MICROLITER OF RESERVOIR SOLUTION (30% (W/V) PEG 4000, 300 MM LI2SO4, 100 MM TRIS-HCL, PH 8.5) AGAINST 700 MICROLITER OF RESERVOIR SOLUTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.93→40 Å / Num. obs: 29097 / % possible obs: 96.9 % / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.3
Reflection shellResolution: 1.93→2.06 Å / Redundancy: 4.73 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLP

1qlp


Resolution: 1.93→37.42 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.9 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ZERO OCCUPANCIES SET FOR SIDE CHAINS WHERE NO DENSITY WAS SEEN.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2328 8 %RANDOM
Rwork0.21 ---
obs0.214 26770 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å2-1.14 Å2
2--3.6 Å20 Å2
3----2.54 Å2
Refinement stepCycle: LAST / Resolution: 1.93→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 26 174 2938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222735
X-RAY DIFFRACTIONr_bond_other_d0.0020.021825
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9793721
X-RAY DIFFRACTIONr_angle_other_deg0.88634437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07125114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25415450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.47158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02537
X-RAY DIFFRACTIONr_nbd_refined0.2040.2540
X-RAY DIFFRACTIONr_nbd_other0.1840.21883
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21324
X-RAY DIFFRACTIONr_nbtor_other0.0890.21494
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3240.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8071.52200
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97122739
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6531204
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0854.5982
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→2.03 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.329 335
Rwork0.276 3862
Refinement TLS params.Method: refined / Origin x: 42.8253 Å / Origin y: 1.2494 Å / Origin z: 10.5905 Å
111213212223313233
T-0.1947 Å2-0.0184 Å20.0045 Å2--0.2585 Å2-0.0059 Å2---0.114 Å2
L1.9464 °2-0.0813 °20.26 °2-1.6899 °20.2691 °2--4.2996 °2
S0.0214 Å °-0.16 Å °-0.0445 Å °0.1677 Å °0.0687 Å °-0.0076 Å °-0.2295 Å °0.2618 Å °-0.0901 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 54
2X-RAY DIFFRACTION1A57 - 157
3X-RAY DIFFRACTION1A160 - 297
4X-RAY DIFFRACTION1A310 - 328
5X-RAY DIFFRACTION1A339 - 374
6X-RAY DIFFRACTION1A1375

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