[English] 日本語
Yorodumi
- PDB-3zxp: Structural and Functional Analyses of the Bro1 Domain Protein BROX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zxp
TitleStructural and Functional Analyses of the Bro1 Domain Protein BROX
ComponentsBRO1 DOMAIN-CONTAINING PROTEIN BROX
KeywordsPROTEIN TRANSPORT
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
BRO1 domain-containing protein BROX
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.495 Å
AuthorsZhai, Q. / Landesman, M.B. / Sundquist, W.I. / Hill, C.P.
CitationJournal: Plos One / Year: 2011
Title: Structure of the Bro1 Domain Protein Brox and Functional Analyses of the Alix Bro1 Domain in HIV-1 Budding.
Authors: Zhai, Q. / Landesman, M.B. / Robinson, H. / Sundquist, W.I. / Hill, C.P.
History
DepositionAug 13, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Other
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BRO1 DOMAIN-CONTAINING PROTEIN BROX
B: BRO1 DOMAIN-CONTAINING PROTEIN BROX
C: BRO1 DOMAIN-CONTAINING PROTEIN BROX


Theoretical massNumber of molelcules
Total (without water)138,2233
Polymers138,2233
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-22.8 kcal/mol
Surface area51700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.064, 67.164, 103.865
Angle α, β, γ (deg.)90.00, 96.95, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein BRO1 DOMAIN-CONTAINING PROTEIN BROX / BRO1 DOMAIN- AND CAAX MOTIF-CONTAINING PROTEIN / BROX


Mass: 46074.441 Da / Num. of mol.: 3 / Fragment: BRO1, RESIDUES 1-401
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET151/D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: Q5VW32
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 38.3 % / Description: NONE
Crystal growpH: 6.6 / Details: 22% PEG 1500, 0.1M MMT 6.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.54178
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2008
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 54427 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 51.46 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 96.5

-
Processing

Software
NameClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
REFMACphasing
PHENIXrefinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.495→27.374 Å / SU ML: 0.81 / σ(F): 1.35 / Phase error: 26.48 / Stereochemistry target values: ML / Details: RESIDUES 379-389 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2474 2710 5.1 %
Rwork0.2014 --
obs0.2037 53119 97.17 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.585 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 60.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.0127 Å20 Å2-4.8156 Å2
2--2.2112 Å20 Å2
3----1.8213 Å2
Refinement stepCycle: LAST / Resolution: 2.495→27.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9269 0 0 30 9299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049499
X-RAY DIFFRACTIONf_angle_d0.72412861
X-RAY DIFFRACTIONf_dihedral_angle_d13.1653525
X-RAY DIFFRACTIONf_chiral_restr0.0511397
X-RAY DIFFRACTIONf_plane_restr0.0031648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4951-2.54050.41951300.32562333X-RAY DIFFRACTION87
2.5405-2.58930.38731310.30212638X-RAY DIFFRACTION96
2.5893-2.64210.3041420.272619X-RAY DIFFRACTION97
2.6421-2.69950.31761540.27512650X-RAY DIFFRACTION97
2.6995-2.76230.32071570.2582581X-RAY DIFFRACTION97
2.7623-2.83130.33831350.25022645X-RAY DIFFRACTION97
2.8313-2.90770.27131580.24692628X-RAY DIFFRACTION97
2.9077-2.99320.30841270.23592643X-RAY DIFFRACTION97
2.9932-3.08970.32761430.24512675X-RAY DIFFRACTION98
3.0897-3.20.3331400.23882657X-RAY DIFFRACTION98
3.2-3.32790.24441580.23292644X-RAY DIFFRACTION98
3.3279-3.47910.25341300.21842664X-RAY DIFFRACTION98
3.4791-3.66210.27791240.21342700X-RAY DIFFRACTION98
3.6621-3.89090.24831460.20942705X-RAY DIFFRACTION98
3.8909-4.19040.22671490.18432706X-RAY DIFFRACTION99
4.1904-4.61020.20521470.15012696X-RAY DIFFRACTION99
4.6102-5.27320.19691330.15282749X-RAY DIFFRACTION99
5.2732-6.62810.24031640.20612742X-RAY DIFFRACTION99
6.6281-27.3760.16561420.15072734X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.2734-0.02090.2650.3964-0.14240.1101-0.019-0.0910.33-0.1605-0.1354-0.0994-0.35560.14440.38980.601-0.1331-0.00340.2237-0.03970.310461.757548.85165.6234
20.2356-0.1514-0.14860.29380.00620.1407-0.07290.0292-0.0345-0.0912-0.07450.1999-0.3665-0.1006-0.86760.77810.1834-0.12080.0742-0.00480.265747.867249.8721-9.0636
30.11190.13990.01040.21240.10890.3481-0.06070.1693-0.011-0.1841-0.11230.0045-0.32760.1857-0.58310.6295-0.05310.0721-0.00640.1365-0.010557.014542.705-6.224
40.25410.08760.08970.22080.04090.4292-0.0761-0.1354-0.0747-0.1886-0.00240.0646-0.27540.2725-0.00190.4505-0.0171-0.00120.1727-0.02120.258560.79836.53040.6243
50.3831-0.10240.36110.1864-0.13740.404-0.1515-0.02680.02590.0354-0.0317-0.1692-0.40360.3692-0.02620.2642-0.1258-0.0110.24190.03250.207572.324337.93619.5833
60.2393-0.0583-0.10540.14390.08090.1759-0.0083-0.1189-0.25360.00650.05610.0445-0.18170.0163-00.4217-0.0685-0.10750.38340.00880.36673.796734.272134.4301
70.07680.11020.06990.14040.08820.0551-0.10230.03870.0627-0.1069-0.0970.02790.0357-0.092300.51770.0521-0.08150.2094-0.0470.296845.125738.7533-14.4178
80.0363-0.01130.00480.02090.00060.00070.0010.0150.0439-0.05470.1531-0.10740.04490.0061-0.00080.7807-0.1097-0.15730.46770.09090.554165.533255.9899-4.0132
90.2696-0.1088-0.0620.2230.15380.425-0.2796-0.11050.04290.25370.1155-0.1289-0.215-0.2386-0.09420.52010.1119-0.01540.52740.10530.553615.50438.440960.5702
100.02470.0142-0.01380.06440.05580.0665-0.1287-0.36930.19270.2848-0.0376-0.0022-0.1887-0.1194-0.00010.60170.13470.05450.6511-0.06920.501911.775634.464277.1558
110.0138-0.0001-0.01050.01870.00880.01210.17080.1712-0.01380.17580.2593-0.01320.23850.0429-0.00070.64210.05040.05690.85020.08290.69426.720515.237477.9797
120.151-0.20120.19750.3039-0.13360.5732-0.1118-0.1404-0.00070.19550.130.0412-0.0683-0.2884-0.00010.23460.01520.06350.40330.05460.484915.041831.067762.5958
130.1379-0.14850.07740.1664-0.14480.4655-0.07140.0193-0.1281-0.0128-0.0359-0.0780.1683-0.054400.2672-0.07370.02010.37640.03610.410124.633428.163748.5841
140.11920.0925-0.04390.0908-0.13750.5622-0.01390.09470.0206-0.15650.05470.0972-0.1261-0.34160.0030.31180.01620.00540.47550.05850.468227.410134.075436.73
150.40710.19370.22430.2588-0.14480.4698-0.06740.03720.04090.05720.10170.23050.0240.0032-00.4136-0.01520.08280.34070.04890.444238.140335.239233.9248
160.1650.17470.13790.1880.15090.12030.2118-0.13170.21440.01080.0864-0.0181-0.0877-0.27450.15710.32590.05460.16540.41650.19330.401112.405127.830473.3163
170.26940.4669-0.43671.3296-0.28941.16810.3024-0.07220.3310.0476-0.02190.2037-0.2523-0.06420.56660.30380.1093-0.00340.6186-0.19640.403790.502537.823273.9482
180.02550.0318-0.02340.0396-0.03050.03870.0933-0.06780.2207-0.1645-0.1298-0.0369-0.28850.3109-00.4014-0.0578-0.04560.5227-0.1630.5989114.871739.326470.0183
190.42260.2733-0.01950.2158-0.10070.3922-0.0521-0.46790.1670.02880.0175-0.0073-0.04830.0392-0.00010.23920.0333-0.05250.4408-0.04780.384899.799533.82869.3552
200.4990.0132-0.24780.25150.1430.2088-0.1762-0.2374-0.06810.03880.1395-0.0543-0.1809-0.03980.00010.2620.0425-0.03850.38220.0160.36887.95828.208266.7482
210.27670.1249-0.13220.19520.05990.15820.0226-0.2501-0.12370.0568-0.00340.04810.051-0.1587-0.00010.3024-0.00650.01250.46080.05370.311373.657426.556766.1938
220.52730.1774-0.15250.43020.03010.299-0.0242-0.54160.1890.13580.06740.0938-0.0413-0.0337-0.05240.27880.0610.04140.6562-0.0070.270764.819929.788170.8401
230.2409-0.1256-0.09890.16850.00130.2706-0.256-0.13720.07950.03070.2657-0.0249-0.0938-0.278200.37130.11530.05160.55270.050.614856.111530.936463.9706
240.12170.0601-0.03180.3263-0.27320.2274-0.1265-0.16990.1291-0.0139-0.0150.026-0.0160.1335-0.00620.15240.0374-0.01650.4486-0.18040.299105.255631.413265.8978
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID -3:19)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 20:67)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 68:137)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 138:182)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 183:307)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 308:351)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 352:378)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 390:401)
9X-RAY DIFFRACTION9(CHAIN B AND RESID -1:20)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 21:70)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 71:83)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 84:168)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 169:230)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 231:298)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 299:349)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 350:398)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 2:18)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 19:45)
19X-RAY DIFFRACTION19(CHAIN C AND RESID 46:135)
20X-RAY DIFFRACTION20(CHAIN C AND RESID 136:197)
21X-RAY DIFFRACTION21(CHAIN C AND RESID 198:234)
22X-RAY DIFFRACTION22(CHAIN C AND RESID 235:300)
23X-RAY DIFFRACTION23(CHAIN C AND RESID 301:347)
24X-RAY DIFFRACTION24(CHAIN C AND RESID 348:397)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more