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- PDB-3r9m: Crystal structure of the Brox Bro1 domain -

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Basic information

Entry
Database: PDB / ID: 3r9m
TitleCrystal structure of the Brox Bro1 domain
ComponentsBRO1 domain-containing protein BROX
KeywordsPROTEIN BINDING / Bro1 domain
Function / homology
Function and homology information


mitotic nuclear membrane reassembly / nuclear envelope / nuclear membrane / extracellular exosome
Similarity search - Function
BRO1 domain-containing protein BROX / alix/aip1 like domains / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / BRO1 domain-containing protein BROX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMu, R.L. / Jiang, J.S. / Snyder, G. / Smith, P. / Xiao, T.
CitationJournal: Structure / Year: 2011
Title: The Phe105 Loop of Alix Bro1 Domain Plays a Key Role in HIV-1 Release.
Authors: Sette, P. / Mu, R. / Dussupt, V. / Jiang, J. / Snyder, G. / Smith, P. / Xiao, T.S. / Bouamr, F.
History
DepositionMar 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Sep 13, 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 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BRO1 domain-containing protein BROX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,46420
Polymers42,4611
Non-polymers1,00319
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)189.204, 189.204, 49.523
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein BRO1 domain-containing protein BROX / BRO1 domain- and CAAX motif-containing protein


Mass: 42461.238 Da / Num. of mol.: 1 / Fragment: UNP residues 2-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BROX, BROFTI, C1orf58 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5VW32
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

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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: 6.03 Å3/Da / Density % sol: 79.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 1M sodium formate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 74628 / Num. obs: 74479 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.18 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.95-1.981100
1.98-2.021100
2.02-2.06199.9
2.06-2.11100
2.1-2.151100
2.15-2.21100
2.2-2.251100
2.25-2.31199.9
2.31-2.381100
2.38-2.46199.9
2.46-2.54199.9
2.54-2.65199.9
2.65-2.771100
2.77-2.91199.9
2.91-3.1199.9
3.1-3.33199.9
3.33-3.67199.8
3.67-4.2199.7
4.2-5.29199.6
5.29-50198

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OEW

2oew


Resolution: 1.95→47.301 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 15.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1671 1892 2.69 %RANDOM
Rwork0.1489 ---
all0.1494 74432 --
obs0.1494 70421 94.61 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5711 Å2-0 Å2-0 Å2
2--2.5711 Å2-0 Å2
3----4.6258 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.95→47.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2992 0 65 452 3509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123172
X-RAY DIFFRACTIONf_angle_d1.4024275
X-RAY DIFFRACTIONf_dihedral_angle_d14.1641177
X-RAY DIFFRACTIONf_chiral_restr0.103460
X-RAY DIFFRACTIONf_plane_restr0.008548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99880.24421290.21744499X-RAY DIFFRACTION88
1.9988-2.05280.22611300.19484646X-RAY DIFFRACTION90
2.0528-2.11320.18571280.17514611X-RAY DIFFRACTION90
2.1132-2.18140.17681330.16384753X-RAY DIFFRACTION93
2.1814-2.25940.18311310.16284748X-RAY DIFFRACTION92
2.2594-2.34980.18591290.16314764X-RAY DIFFRACTION92
2.3498-2.45680.21721350.16634824X-RAY DIFFRACTION94
2.4568-2.58630.19021330.17054882X-RAY DIFFRACTION95
2.5863-2.74830.17991340.15935024X-RAY DIFFRACTION97
2.7483-2.96050.17821420.16075017X-RAY DIFFRACTION98
2.9605-3.25840.17031390.1535104X-RAY DIFFRACTION98
3.2584-3.72970.16111410.13925156X-RAY DIFFRACTION99
3.7297-4.69840.13561410.11655191X-RAY DIFFRACTION99
4.6984-47.31490.14281470.13935310X-RAY DIFFRACTION98

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