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- PDB-4bb2: Crystal structure of cleaved corticosteroid-binding globulin in c... -

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Basic information

Entry
Database: PDB / ID: 4bb2
TitleCrystal structure of cleaved corticosteroid-binding globulin in complex with progesterone
Components(CORTICOSTEROID-BINDING ...) x 2
KeywordsTRANSPORT PROTEIN / SERPINS / STEROID BINDING
Function / homology
Function and homology information


glucocorticoid biosynthetic process / Glucocorticoid biosynthesis / 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
CYSTEINE / PROGESTERONE / Corticosteroid-binding globulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsGardill, B.R. / Vogl, M.R. / Lin, H. / Hammond, G.L. / Muller, Y.A.
CitationJournal: Plos One / Year: 2012
Title: Corticosteroid-Binding Globulin: Structure-Function Implications from Species Differences
Authors: Gardill, B.R. / Vogl, M.R. / Lin, H. / Hammond, G.L. / Muller, Y.A.
History
DepositionSep 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Dec 20, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CORTICOSTEROID-BINDING GLOBULIN
B: CORTICOSTEROID-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3329
Polymers41,5862
Non-polymers7467
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-31.7 kcal/mol
Surface area15340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.190, 122.700, 81.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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CORTICOSTEROID-BINDING ... , 2 types, 2 molecules AB

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


Mass: 37502.410 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-371 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-2T HCBG K126A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P08185
#2: Protein/peptide CORTICOSTEROID-BINDING GLOBULIN / CBG / SERPIN A6 / TRANSCORTIN


Mass: 4083.906 Da / Num. of mol.: 1 / Fragment: RESIDUES 373-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-2T HCBG K126A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P08185

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Non-polymers , 4 types, 118 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#5: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2 / Comment: hormone*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.07 %
Description: DIFFRACTION PATTERN IMPROVED AFTER A 2 SEC AND A 4 SEC CRYSTAL ANNEALING STEP.
Crystal growpH: 7.5 / Details: 0.1 M HEPES 7.5, 2 % PEG 400, 2 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 12, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.48→35 Å / Num. obs: 16184 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.9
Reflection shellResolution: 2.48→2.63 Å / Redundancy: 7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.2 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VDY

2vdy


Resolution: 2.48→34.07 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 16.864 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.509 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23393 1619 10 %RANDOM
Rwork0.17718 ---
obs0.18293 14563 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.83 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å20 Å2
2--0.52 Å20 Å2
3----2.6 Å2
Refinement stepCycle: LAST / Resolution: 2.48→34.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 49 111 3024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192980
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9624038
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4515364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73524.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03915501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.521511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212194
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.482→2.546 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 113 -
Rwork0.241 1012 -
obs--95.42 %
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)
12.0192-1.2361-1.93632.17881.79384.86670.09630.0640.1965-0.08980.03390.0233-0.28440.0152-0.13020.1807-0.0184-0.0280.00880.00970.1421-23.5906-7.021216.7746
28.6176-6.1992-4.399611.601-1.09999.7747-0.1520.72170.36670.11460.13860.7347-0.1366-0.63430.01340.13290.0064-0.03290.24310.08110.3176-36.9011-9.325619.5468
35.05960.19923.1512.9384-1.301110.7705-0.30090.2835-0.1587-0.2890.08250.20150.1301-0.3550.21840.2119-0.0160.02590.1299-0.00280.3142-28.3402-22.2423.5491
45.8136-3.9883-0.593710.353-3.64046.7386-0.1274-0.3469-0.07820.4820.21280.44050.3359-0.1103-0.08540.2093-0.04940.02420.09190.03770.1539-32.9094-16.615533.0761
55.2353-0.22241.11237.81043.296718.3245-0.0926-0.4246-0.19620.2094-0.2496-0.33270.25251.10790.34220.20060.0364-0.05050.15040.07610.228-15.5005-24.514230.4905
61.2613-0.3107-0.84211.21320.9163.33290.0424-0.03520.00260.04020.1034-0.33440.15720.381-0.14570.12980.0373-0.04510.05440.00420.2569-11.223-24.16945.7397
70.77030.11080.27534.74660.03831.91160.03010.0380.0093-0.3824-0.0255-0.0141-0.11270.0555-0.00460.1493-0.00390.01080.0042-0.01130.1417-17.7618-14.3031-4.7917
80.6291-0.0439-0.19412.89452.8245.4189-0.0006-0.14120.24140.10080.2212-0.1015-0.3060.4603-0.22060.1712-0.0181-0.04250.0829-0.02160.2413-19.2398-6.125929.0287
91.213-0.3282-0.92192.18161.82424.66380.05890.03180.0585-0.0359-0.0522-0.02470.1181-0.0956-0.00670.13280.0057-0.01110.00290.00720.1784-17.0902-18.7868.1671
109.77270.8975-4.46294.44882.04535.70280.1111-0.482-0.04540.12270.0196-0.59530.12470.8992-0.13070.25060.0252-0.08390.21520.02380.2309-11.1083-17.39987.3494
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 77
2X-RAY DIFFRACTION2A78 - 90
3X-RAY DIFFRACTION3A91 - 114
4X-RAY DIFFRACTION4A115 - 136
5X-RAY DIFFRACTION5A137 - 168
6X-RAY DIFFRACTION6A169 - 214
7X-RAY DIFFRACTION7A215 - 282
8X-RAY DIFFRACTION8A283 - 322
9X-RAY DIFFRACTION9A323 - 349
10X-RAY DIFFRACTION9B - A351 - 373
11X-RAY DIFFRACTION10B374 - 383

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