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- PDB-2vdy: Crystal structure of the reactive loop cleaved Corticosteroid Bin... -

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Basic information

Entry
Database: PDB / ID: 2vdy
TitleCrystal structure of the reactive loop cleaved Corticosteroid Binding Globulin complexed with Cortisol
ComponentsCORTICOSTEROID-BINDING GLOBULIN
KeywordsTRANSPORT PROTEIN / GLYCOPROTEIN / LIPID-BINDING / STEROID-BINDING / DISEASE MUTATION / CORTICOSTEROID BINDING GLOBULIN / CBG / SERPIN / CLEAVED / SECRETED / CORTISOL / TRANSPORT
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
Chem-HCY / Corticosteroid-binding globulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhou, A. / Wei, Z. / Read, R.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The S-to-R Transition of Corticosteroid-Binding Globulin and the Mechanism of Hormone Release.
Authors: Zhou, A. / Wei, Z. / Stanley, P.L. / Read, R.J. / Stein, P.E. / Carrell, R.W.
History
DepositionOct 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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
B: CORTICOSTEROID-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0964
Polymers83,3712
Non-polymers7252
Water2,972165
1
A: CORTICOSTEROID-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0482
Polymers41,6861
Non-polymers3621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CORTICOSTEROID-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0482
Polymers41,6861
Non-polymers3621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.673, 39.757, 111.586
Angle α, β, γ (deg.)83.09, 85.70, 69.42
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 41685.590 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-405 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH CORTISOL / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSUMO3-CBG / Production host: Escherichia coli BL21(DE3) COLI, / References: UniProt: P08185
#2: Chemical ChemComp-HCY / (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione / CORTISOL / Cortisol


Mass: 362.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30O5 / Comment: medication, hormone*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE REACTIVE LOOP OF THE PROTEIN FOR BOTH CHAINS A AND B (CORRESPONDING TO UNIPROT RESIDUES 358-371) ...THE REACTIVE LOOP OF THE PROTEIN FOR BOTH CHAINS A AND B (CORRESPONDING TO UNIPROT RESIDUES 358-371) HAVE BEEN MUTATED AND ARE NOW REPLACED BY PDB RESIDUES 336-349. SEE ALSO REMARK 999.
Nonpolymer details(8S,9S,10R,11S,13S,14S,17R)-11, 17-DIHYDROXY-17-(2-HYDROXYACETYL)-10,13-DIMETHYL-2,6,7,8,9, ...(8S,9S,10R,11S,13S,14S,17R)-11, 17-DIHYDROXY-17-(2-HYDROXYACETYL)-10,13-DIMETHYL-2,6,7,8,9, 11,12,14,15,16-DECAHYDRO-1H-CYCLOPENTA[A]PHENANTHREN-3-ONE (HCY): CORTISOL
Sequence detailsRESIDUES 336-349 OF HUMAN CBG MUTATED TO TEAAGAMFLEAIPR. THIS PROTEIN WAS CLEAVED BY THROMBIN AT ...RESIDUES 336-349 OF HUMAN CBG MUTATED TO TEAAGAMFLEAIPR. THIS PROTEIN WAS CLEAVED BY THROMBIN AT ARG349 BEFORE CRYSTALLISATION. SEE ALSO REMARK 400.

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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: 1.93 Å3/Da / Density % sol: 34 % / Description: NONE
Crystal growpH: 7.4 / Details: 10-20% PEG3350, 0.2M NACL, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5419
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.3→19.4 Å / Num. obs: 22575 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.5 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMN

1qmn


Resolution: 2.3→19.43 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 19.362 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.431 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1295 5.1 %RANDOM
Rwork0.21 ---
obs0.213 24274 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.29 Å21.45 Å2
2--1.36 Å20.74 Å2
3----2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5670 0 52 165 5887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225846
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9691.9657937
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0635714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44624.821251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43515996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7321518
X-RAY DIFFRACTIONr_chiral_restr0.0610.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024306
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1540.22451
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.23996
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0910.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.181.53719
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.30825798
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.31832425
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.4984.52139
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 80 -
Rwork0.273 1639 -
obs--86.34 %
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)
10.7028-0.3032-0.49861.01290.73832.3766-0.00010.00520.0069-0.01980.0107-0.06870.0347-0.0249-0.0105-0.1688-0.0269-0.0305-0.13660.0221-0.0692-18.326816.7645-39.2394
20.83650.0626-1.13280.7021-0.49695.0348-0.01370.05440.0347-0.0064-0.04150.02870.24-0.00690.0553-0.06270.00280-0.0895-0.012-0.0411-8.63726.182716.6819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 383
2X-RAY DIFFRACTION2B20 - 383

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