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- PDB-4w7y: Dimeric BAP29 vDED with disulfide bonds in crystal contacts -

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Basic information

Entry
Database: PDB / ID: 4w7y
TitleDimeric 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
ACETATE ION / B-cell receptor-associated protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,7585
Polymers15,4622
Non-polymers2953
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-50 kcal/mol
Surface area10130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.870, 118.870, 30.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 7731.090 Da / Num. of mol.: 2 / 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.04 Å3/Da / Density % sol: 69.56 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion / pH: 4.6
Details: Grown in 34% 2-methyl-2,4-pentanediol (MPD), 100 mM Na acetate pH 4.6 and 20 mM CaCl2 using SeMet labeled protein purified in 20 mM Tris pH 8, 150 mM NaCl and 2 mM tris(2-carboxyethyl) ...Details: Grown in 34% 2-methyl-2,4-pentanediol (MPD), 100 mM Na acetate pH 4.6 and 20 mM CaCl2 using SeMet labeled protein purified in 20 mM Tris pH 8, 150 mM NaCl and 2 mM tris(2-carboxyethyl)phosphine (TECEP) and concentrated to ~13 mg/mL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→34.31 Å / Num. obs: 16720 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rsym value: 0.072 / Net I/σ(I): 17.09
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.93 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→34.315 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 787 4.71 %Random
Rwork0.1953 ---
obs0.1973 16718 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→34.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 20 31 1095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121065
X-RAY DIFFRACTIONf_angle_d1.2751411
X-RAY DIFFRACTIONf_dihedral_angle_d17.189440
X-RAY DIFFRACTIONf_chiral_restr0.053158
X-RAY DIFFRACTIONf_plane_restr0.006183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.65670.27011090.2552651X-RAY DIFFRACTION100
2.6567-2.86180.29641430.23112659X-RAY DIFFRACTION100
2.8618-3.14960.26051390.222648X-RAY DIFFRACTION100
3.1496-3.60490.27071210.20572667X-RAY DIFFRACTION100
3.6049-4.54020.22291320.17022667X-RAY DIFFRACTION100
4.5402-34.3180.20491430.18312639X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 71.3112 Å / Origin y: -8.0539 Å / Origin z: 3.9062 Å
111213212223313233
T0.7042 Å20.1281 Å2-0.0007 Å2-0.3975 Å20.0776 Å2--0.5048 Å2
L1.2608 °2-1.9849 °20.4097 °2-5.6933 °2-0.9965 °2--0.4455 °2
S0.0137 Å °-0.1544 Å °-0.3698 Å °-0.4709 Å °0.0961 Å °-0.1191 Å °0.4826 Å °0.1735 Å °-0.1445 Å °
Refinement TLS groupSelection details: chain 'A' or chain 'B'

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