[English] 日本語
Yorodumi
- PDB-1ztp: X-ray structure of gene product from homo sapiens Hs.433573 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ztp
TitleX-ray structure of gene product from homo sapiens Hs.433573
ComponentsBasophilic leukemia expressed protein BLES03
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hs.433573 / P5326 / BLES03 / BC010512 / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / Center for Eukaryotic Structural Genomics
Function / homologyBasophilic leukemia-expressed protein Bles03-like / Basophilic leukemia-expressed protein Bles03 / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Translation Initiation factor eIF- 4e-like / RNA binding / 2-Layer Sandwich / Alpha Beta / UPF0696 protein C11orf68
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsWesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: The structure at 2.5 A resolution of human basophilic leukemia-expressed protein BLES03.
Authors: Bitto, E. / Bingman, C.A. / Robinson, H. / Allard, S.T. / Wesenberg, G.E. / Phillips, G.N.
History
DepositionMay 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Remark 300 BIOMOLECULE: 1, 2, 3 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1, 2, 3 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE THREE COPIES OF THE APPARENT MONOMERIC FORM OF THE BIOLOGICAL MOLECULE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Basophilic leukemia expressed protein BLES03
B: Basophilic leukemia expressed protein BLES03
C: Basophilic leukemia expressed protein BLES03


Theoretical massNumber of molelcules
Total (without water)82,8013
Polymers82,8013
Non-polymers00
Water3,909217
1
A: Basophilic leukemia expressed protein BLES03


Theoretical massNumber of molelcules
Total (without water)27,6001
Polymers27,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Basophilic leukemia expressed protein BLES03


Theoretical massNumber of molelcules
Total (without water)27,6001
Polymers27,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Basophilic leukemia expressed protein BLES03


Theoretical massNumber of molelcules
Total (without water)27,6001
Polymers27,6001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
4
A: Basophilic leukemia expressed protein BLES03

C: Basophilic leukemia expressed protein BLES03


Theoretical massNumber of molelcules
Total (without water)55,2012
Polymers55,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
Buried area5950 Å2
ΔGint-19 kcal/mol
Surface area31980 Å2
MethodPISA
5
A: Basophilic leukemia expressed protein BLES03
B: Basophilic leukemia expressed protein BLES03


Theoretical massNumber of molelcules
Total (without water)55,2012
Polymers55,2012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-13 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.547, 116.809, 123.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
12A
22C

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111MSEGLYAA30 - 8330 - 83
211MSEGLYBB30 - 8330 - 83
311MSEGLYCC30 - 8330 - 83
421ASPLEUAA92 - 25092 - 250
521ASPLEUBB92 - 25092 - 250
621ASPLEUCC92 - 25092 - 250
112GLNGLYAA84 - 9184 - 91
212GLNGLYCC84 - 9184 - 91

NCS ensembles :
ID
1
2

-
Components

#1: Protein Basophilic leukemia expressed protein BLES03


Mass: 27600.342 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Hs.433573 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q9H3H3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10 MG/ML PROTEIN, 1.2 M SODIUM CITRATE, 0.100 M TRIS, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC / Detector: CCD / Date: May 5, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
RadiationMonochromator: CRYOGENICALLY COOLED SI (111) DOUBLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 12.3 % / Av σ(I) over netI: 13.35 / Number: 31664 / Rmerge(I) obs: 0.106 / Χ2: 1.05 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 31664 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
6.165010010.0480.962
4.896.1610010.0640.947
4.274.8910010.0681.041
3.884.2710010.0750.982
3.613.8810010.0851.053
3.393.6199.910.1011.165
3.223.3999.710.1271.178
3.083.2299.610.1621.166
2.963.089910.211.127
2.862.9699.110.2681.073
2.772.8698.710.3391.04
2.692.7797.710.3951.054
2.622.6995.910.4690.998
2.562.6295.210.5080.982
2.52.5693.110.5970.94
ReflectionResolution: 2.5→50 Å / Num. obs: 31664 / % possible obs: 98.6 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 13.353
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 9 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.675 / % possible all: 93.1

-
Phasing

PhasingMethod: SAD
Phasing MADD res high: 3.69 Å / D res low: 43.98 Å / FOM : 0.299 / FOM acentric: 0.327 / FOM centric: 0 / Reflection: 18562
Phasing MAD setR cullis: 0.735 / R cullis acentric: 0.703 / R cullis centric: 10 / R kraut: 0.02 / R kraut acentric: 0.02 / R kraut centric: 0.022 / Highest resolution: 3.69 Å / Lowest resolution: 43.98 Å / FOM : 0.299 / FOM acentric: 0.328 / FOM centric: 0 / Loc: 20.483 / Loc acentric: 20.507 / Loc centric: 20.466 / Power: 1.399 kW / Power acentric: 1.378 / Power centric: 1.602
Phasing MAD set shell

ID: 1 / R cullis centric: 10 / FOM centric: 0

Resolution (Å)R cullisR cullis acentricR krautR kraut acentricR kraut centricFOM FOM acentricLocLoc acentricLoc centricPower (kW)Power acentricPower centric
7.37-43.980.560.510.0240.0230.0290.3870.46621.01221.05621.2482.1842.1882.165
5.85-7.370.6020.570.0270.0270.0350.3980.44418.0318.04118.1211.9741.9582.103
5.12-5.850.6890.6590.0220.0220.0250.3490.38218.69618.70818.8061.5971.5971.594
4.65-5.120.7660.7370.0170.0180.0160.3130.33819.87719.88219.9291.3221.321.35
4.32-4.650.8120.7810.0160.0160.0120.2690.29121.00521.01321.0891.1331.1361.094
4.06-4.320.8490.820.0170.0170.0140.2410.25821.06521.0721.1270.960.9571
3.86-4.060.8920.8640.0190.0190.0140.2230.23821.99222.00122.0950.8250.8230.851
3.69-3.860.9020.8770.020.0210.0140.2050.21822.37222.37222.3720.7360.7360.742
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflection
7.37-43.980.38810.466602348
5.85-7.370.39730.442302330
5.12-5.850.34860.381202349
4.65-5.120.31230.337502336
4.32-4.650.26860.2902332
4.06-4.320.23940.256102347
3.86-4.060.22280.237702334
3.69-3.860.20630.218202186
Phasing dmFOM : 0.59 / FOM acentric: 0.59 / FOM centric: 0.59 / Reflection: 31594 / Reflection acentric: 28112 / Reflection centric: 3482
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-43.9670.930.930.815081083425
4.5-7.10.860.880.7443623664698
3.6-4.50.840.850.7653904747643
3.1-3.60.70.710.653724835537
2.7-3.10.440.440.3894158629786
2.5-2.70.220.220.2255475154393

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.401data extraction
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.124 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.27 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1607 5.103 %RANDOM
Rwork0.188 ---
obs0.19118 31489 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--0.987 Å20 Å2
3----0.637 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5296 0 0 217 5513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225440
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9487420
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.285680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54522.727242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30215823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9841547
X-RAY DIFFRACTIONr_chiral_restr0.0980.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024229
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.22245
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.23673
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.2120
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.75123460
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.33855432
X-RAY DIFFRACTIONr_scbond_it5.90382303
X-RAY DIFFRACTIONr_scangle_it7.9101988
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1615loose positional0.815
12B1615loose positional0.95
13C1615loose positional0.65
21A56loose positional0.575
22C56loose positional0.575
14A1615loose thermal7.7310
15B1615loose thermal5.3110
16C1615loose thermal5.3710
21A56loose thermal3.5710
22C56loose thermal3.5710
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 118 -
Rwork0.275 1902 -
obs--86.96 %

+
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://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