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- PDB-4w80: Tetrameric BAP29 vDED with disulfide bonds in crystal contacts -

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Basic information

Entry
Database: PDB / ID: 4w80
TitleTetrameric BAP29 vDED with disulfide bonds in crystal contacts
ComponentsB-cell receptor-associated protein 29
KeywordsTRANSPORT PROTEIN / Coiled coil / nanomaterial
Function / homology
Function and homology information


protein localization to endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / osteoblast differentiation / apoptotic process / endoplasmic reticulum membrane / membrane
Similarity search - Function
B-cell receptor-associated protein 29/31 / BAP29/BAP31, transmembrane domain / Bap31/Bap29 cytoplasmic coiled-coil domain / Bap31/Bap29 transmembrane region / Bap31/Bap29 cytoplasmic coiled-coil domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
B-cell receptor-associated protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsQuistgaard, E.M.
CitationJournal: Chem.Commun.(Camb.) / Year: 2014
Title: A disulfide polymerized protein crystal.
Authors: Quistgaard, E.M.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B-cell receptor-associated protein 29
B: B-cell receptor-associated protein 29
C: B-cell receptor-associated protein 29
D: B-cell receptor-associated protein 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,13514
Polymers30,1744
Non-polymers96110
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-180 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.910, 117.910, 168.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein
B-cell receptor-associated protein 29 / Bap29


Mass: 7543.510 Da / Num. of mol.: 4 / Fragment: UNP residues 168-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAP29, BAP29 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHQ4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.86 Å3/Da / Density % sol: 74.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 4.6
Details: Grown in 1.8 M ammonium sulfate, 100 mM Na acetate pH 4.6 using protein purified in 20 mM Tris pH 8, 150 mM NaCl and 0.5 mM TCEP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.2→41.69 Å / Num. obs: 9752 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Rsym value: 0.187 / Net I/σ(I): 12.21
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 12.2 % / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W7Z

4w7z


Resolution: 3.2→41.687 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 476 4.89 %RANDOM
Rwork0.1985 ---
obs0.1993 9744 96.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→41.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 50 0 2049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052045
X-RAY DIFFRACTIONf_angle_d0.7892716
X-RAY DIFFRACTIONf_dihedral_angle_d13.84838
X-RAY DIFFRACTIONf_chiral_restr0.033299
X-RAY DIFFRACTIONf_plane_restr0.004346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2002-3.6630.27441490.23062927X-RAY DIFFRACTION93
3.663-4.61410.17391600.17473145X-RAY DIFFRACTION99
4.6141-41.6910.22251670.2013196X-RAY DIFFRACTION96
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)
18.5605-3.70970.00193.75450.26571.99690.60280.2588-0.6132-0.5387-0.43160.44040.26320.0229-0.00640.31990.0020.00520.4451-0.0190.2268-29.0229-33.6968-14.0432
27.014-3.3092-0.76223.49680.08172.1530.3941-0.00830.4639-0.2758-0.2719-0.3544-0.38760.2227-0.07860.348-0.0199-0.03090.34410.07280.341-28.0712-22.7051-11.2389
32.4396-1.8927-0.3643.1244-0.35442.07450.5643-0.7905-0.6233-0.0683-0.29080.25770.3049-0.1758-0.12250.3124-0.04150.02150.343-0.00870.3426-30.3121-34.1875-8.0597
43.4311-1.9229-0.16472.9542-0.03972.61590.3159-1.08130.7440.1381-0.0954-0.2241-0.38910.2772-0.02150.38330.0234-0.05910.3753-0.01940.2415-27.2589-25.2098-5.737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

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