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- PDB-2vdx: Crystal Structure of the reactive loop Cleaved Corticosteroid Bin... -

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Basic information

Entry
Database: PDB / ID: 2vdx
TitleCrystal Structure of the reactive loop Cleaved Corticosteroid Binding Globulin
ComponentsCORTICOSTEROID-BINDING GLOBULIN
KeywordsTRANSPORT PROTEIN / CORTISOL BINDING GLOBULIN / GLYCOPROTEIN / LIPID-BINDING / STEROID-BINDING / DISEASE MUTATION / CBG / SERPIN / CLEAVED / SECRETED / CORTISOL
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: 1.84 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 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
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

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)83,4636
Polymers83,3712
Non-polymers924
Water5,206289
1
A: CORTICOSTEROID-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7554
Polymers41,6861
Non-polymers693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CORTICOSTEROID-BINDING GLOBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7092
Polymers41,6861
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.941, 39.740, 112.113
Angle α, β, γ (deg.)81.94, 84.06, 65.39
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
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSUMO3-CBG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PSUMO3 FUSION SYSTEM / References: UniProt: P08185
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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.
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: 1.89 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 7.4 / Details: 10-20% PEG3350, 0.2M NACL, pH 7.4

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.196
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.196 Å / Relative weight: 1
ReflectionResolution: 1.84→55.4 Å / Num. obs: 51706 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.7
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.5 / % possible all: 94.1

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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: 1.84→55.47 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.573 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2643 5.1 %RANDOM
Rwork0.192 ---
obs0.194 49061 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å2-0.34 Å21.06 Å2
2--0.85 Å2-0.22 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 1.84→55.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5703 0 4 289 5996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225880
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9537982
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20324.745255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.993151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8171520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024364
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.22503
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23990
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2304
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1180.214
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5621.53640
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03325897
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6632299
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5284.52076
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: 1.84→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 209 -
Rwork0.292 3582 -
obs--93.98 %
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)
10.35980.0411-0.51540.86610.52642.4112-0.0001-0.056-0.01080.08850.0292-0.01720.05160.0548-0.0292-0.12830.0113-0.01540.00220.0014-0.0303-18.903615.6332-39.2524
20.47050.1149-0.45490.4827-0.46142.81440.02010.04910.0192-0.1912-0.0216-0.00360.1023-0.00270.00150.00860.0071-0.0081-0.1199-0.0059-0.0654-8.13986.335116.4907
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 383
2X-RAY DIFFRACTION2B21 - 383

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