[English] 日本語
Yorodumi
- PDB-4qyb: 2.1 Angstrom resolution crystal structure of uncharacterized prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qyb
Title2.1 Angstrom resolution crystal structure of uncharacterized protein, disulfide-bridged dimer, from Burkholderia cenocepacia J2315
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homologyNinX, bacteriophage P22 / Bacteriophage P22, NinX / DUF2591 domain-containing protein
Function and homology information
Biological speciesBurkholderia cenocepacia J2315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHalavaty, A.S. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Shuvalova, L. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 2.1 Angstrom resolution crystal structure of uncharacterized protein, disulfide-bridged dimer, from Burkholderia cenocepacia J2315
Authors: Halavaty, A.S. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Shuvalova, L. / Joachimiak, A. / Anderson, W.F.
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,9272
Polymers26,9272
Non-polymers00
Water1,40578
1
A: Uncharacterized protein
B: Uncharacterized protein

A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)53,8544
Polymers53,8544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area5230 Å2
ΔGint-10 kcal/mol
Surface area21830 Å2
MethodPISA
2
A: Uncharacterized protein

B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,9272
Polymers26,9272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area1720 Å2
ΔGint-5 kcal/mol
Surface area11810 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-1 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.945, 85.634, 93.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 0 - 118 / Label seq-ID: 7 - 125

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Uncharacterized protein


Mass: 13463.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia J2315 (bacteria)
Strain: J2315 / Gene: BCAM1129 / Plasmid: pMCSG87 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: B4EGA9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein - 9.6 mg/mL in 10 mM Tris-HCl pH 8.3, 250 mM NaCl, 5 mM BME, crystallization - The Classics II Suite C4 (28): 560 mM Sodium citrate pH 7.0, cryo - 25% (v/v) sucrose, VAPOR DIFFUSION, ...Details: protein - 9.6 mg/mL in 10 mM Tris-HCl pH 8.3, 250 mM NaCl, 5 mM BME, crystallization - The Classics II Suite C4 (28): 560 mM Sodium citrate pH 7.0, cryo - 25% (v/v) sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2014 / Details: Be lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 14651 / Num. obs: 14651 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 49.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.3 / Num. unique all: 746 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PUP

4pup


Resolution: 2.1→28.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 16.235 / SU ML: 0.192 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25648 717 5 %RANDOM
Rwork0.21094 ---
obs0.21315 13578 92.1 %-
all-13578 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.647 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0 Å20 Å2
2--5.23 Å20 Å2
3----6.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 0 78 1805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191788
X-RAY DIFFRACTIONr_bond_other_d0.0040.021626
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.952439
X-RAY DIFFRACTIONr_angle_other_deg0.97733734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.565230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58622.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60815230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5931519
X-RAY DIFFRACTIONr_chiral_restr0.0990.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212079
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02426
Refine LS restraints NCS

Ens-ID: 1 / Number: 5727 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 47 -
Rwork0.228 969 -
obs-969 90.96 %
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)
126.8228-5.868-10.67851.6232-0.004520.67630.5640.08521.5843-0.0892-0.1663-0.3502-0.38251.1436-0.39780.1823-0.05480.04580.16950.0850.252.6659-26.737-20.2311
23.1671-1.1665-0.90753.4234-0.26694.86460.030.27640.2945-0.1615-0.0612-0.01-0.55820.05660.03120.2895-0.0226-0.00240.0480.04040.3472-8.4156-16.0657-16.4937
31.6617-0.10580.23042.1786-0.71393.2787-0.1084-0.05640.1838-0.17060.10050.0589-0.2978-0.14080.00790.14940.0157-0.01170.054-0.00630.3137-13.4689-25.3748-6.7193
42.641-0.1776-0.24861.0447-1.7554.7039-0.02640.1189-0.1065-0.2552-0.0202-0.1552-0.20620.01360.04660.3511-0.0070.03850.07280.00310.3808-8.493-29.7192-13.0003
56.0648-2.07950.67735.19321.25718.31540.15160.0357-0.1912-0.3167-0.0260.04420.8383-0.5133-0.12560.2746-0.1496-0.01980.10650.01690.3418-26.4915-63.7865-15.4739
61.27811.67070.73884.2713-1.07743.3591-0.08140.0552-0.1615-0.63020.208-0.20990.83720.0278-0.12660.4022-0.06190.00210.0798-0.04150.3593-18.178-67.5651-9.1995
70.93820.8019-3.20181.9938-2.402311.08460.0969-0.02580.0557-0.08340.00550.0947-0.3884-0.0096-0.10250.06610.0167-0.01630.1944-0.01950.2709-17.624-48.7826-4.7751
80.7882-0.34520.18522.88461.98974.88760.0256-0.07080.1215-0.4273-0.07630.13420.2483-0.34610.05070.1706-0.0299-0.05660.09380.00960.3122-23.1898-55.6265-11.2246
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 3
2X-RAY DIFFRACTION2A4 - 37
3X-RAY DIFFRACTION3A38 - 80
4X-RAY DIFFRACTION4A86 - 118
5X-RAY DIFFRACTION5B0 - 25
6X-RAY DIFFRACTION6B26 - 66
7X-RAY DIFFRACTION7B67 - 87
8X-RAY DIFFRACTION8B88 - 118

+
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