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- PDB-5cdz: Crystal structure of conserpin in the latent state -

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Basic information

Entry
Database: PDB / ID: 5cdz
TitleCrystal structure of conserpin in the latent state
ComponentsConserpin in the latent state
Keywordshydrolase inhibitor / Serine Protease Inhibitor / Aggregation Resistant / Consensus Design / Stability / Latent state / HYDROLASE
Function / homologyAntithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 Å
AuthorsPorebski, B.T. / McGowan, S. / Keleher, S. / Buckle, A.M.
CitationJournal: Sci Rep / Year: 2016
Title: Smoothing a rugged protein folding landscape by sequence-based redesign.
Authors: Porebski, B.T. / Keleher, S. / Hollins, J.J. / Nickson, A.A. / Marijanovic, E.M. / Borg, N.A. / Costa, M.G. / Pearce, M.A. / Dai, W. / Zhu, L. / Irving, J.A. / Hoke, D.E. / Kass, I. / ...Authors: Porebski, B.T. / Keleher, S. / Hollins, J.J. / Nickson, A.A. / Marijanovic, E.M. / Borg, N.A. / Costa, M.G. / Pearce, M.A. / Dai, W. / Zhu, L. / Irving, J.A. / Hoke, D.E. / Kass, I. / Whisstock, J.C. / Bottomley, S.P. / Webb, G.I. / McGowan, S. / Buckle, A.M.
History
DepositionJul 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserpin in the latent state
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7633
Polymers42,5781
Non-polymers1842
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-1 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.679, 101.679, 62.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Conserpin in the latent state


Mass: 42578.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Hepes pH 8.0, 0.2 M Ammonium Acetate, 35% v/v MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2014
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.449→33.282 Å / Num. obs: 65513 / % possible obs: 99.94 % / Redundancy: 38 % / Net I/σ(I): 17.24

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CDX

5cdx


Resolution: 1.449→33.282 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 3319 5.07 %Random selection
Rwork0.1566 ---
obs0.1581 65500 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.449→33.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 12 350 3146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122931
X-RAY DIFFRACTIONf_angle_d1.5683974
X-RAY DIFFRACTIONf_dihedral_angle_d12.6321098
X-RAY DIFFRACTIONf_chiral_restr0.134450
X-RAY DIFFRACTIONf_plane_restr0.012509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.449-1.46970.28511310.23562579X-RAY DIFFRACTION100
1.4697-1.49170.2031290.20992616X-RAY DIFFRACTION100
1.4917-1.5150.24551440.19722531X-RAY DIFFRACTION100
1.515-1.53980.21061640.18632550X-RAY DIFFRACTION100
1.5398-1.56630.21291240.18352629X-RAY DIFFRACTION100
1.5663-1.59480.21731390.17282565X-RAY DIFFRACTION100
1.5948-1.62550.21661380.1722559X-RAY DIFFRACTION100
1.6255-1.65870.22481490.17582610X-RAY DIFFRACTION100
1.6587-1.69470.20631430.17212572X-RAY DIFFRACTION100
1.6947-1.73420.18861340.16942567X-RAY DIFFRACTION100
1.7342-1.77750.20261370.16912579X-RAY DIFFRACTION100
1.7775-1.82560.19461330.15742568X-RAY DIFFRACTION100
1.8256-1.87930.1821400.16082627X-RAY DIFFRACTION100
1.8793-1.940.19291290.16132579X-RAY DIFFRACTION100
1.94-2.00930.16691440.15682578X-RAY DIFFRACTION100
2.0093-2.08970.18481380.15092606X-RAY DIFFRACTION100
2.0897-2.18480.16591280.152591X-RAY DIFFRACTION100
2.1848-2.30.17151270.14662614X-RAY DIFFRACTION100
2.3-2.4440.17061450.15032590X-RAY DIFFRACTION100
2.444-2.63270.17341240.15532609X-RAY DIFFRACTION100
2.6327-2.89750.20641320.15842606X-RAY DIFFRACTION100
2.8975-3.31640.16671500.1542610X-RAY DIFFRACTION100
3.3164-4.1770.17221390.13352620X-RAY DIFFRACTION100
4.177-33.2910.18621580.15632626X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 35.2246 Å / Origin y: -8.5609 Å / Origin z: -4.4714 Å
111213212223313233
T0.106 Å2-0.0384 Å2-0.0053 Å2-0.0975 Å2-0.031 Å2--0.1187 Å2
L0.8185 °2-0.1619 °20.5528 °2-0.8283 °2-0.2757 °2--1.724 °2
S-0.0386 Å °-0.0148 Å °0.0438 Å °0.0566 Å °-0.0254 Å °0.0396 Å °-0.1541 Å °0.0391 Å °0.0558 Å °
Refinement TLS groupSelection details: all

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