[English] 日本語
Yorodumi
- PDB-5nm0: Nb36 Ser85Cys with Hg, crystal form 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nm0
TitleNb36 Ser85Cys with Hg, crystal form 1
ComponentsNb36
KeywordsIMMUNE SYSTEM / Ig domain llama single domain antibody nanobody Hg derivative
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsHansen, S.B. / Andersen, K.R. / Laursen, N.S. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
The Danish Research Council for Independent ResearchDanscatt Denmark
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Introducing site-specific cysteines into nanobodies for mercury labelling allows de novo phasing of their crystal structures.
Authors: Hansen, S.B. / Laursen, N.S. / Andersen, G.R. / Andersen, K.R.
History
DepositionApr 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nb36
B: Nb36
C: Nb36
D: Nb36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7786
Polymers54,3774
Non-polymers4012
Water6,828379
1
A: Nb36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7952
Polymers13,5941
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-16 kcal/mol
Surface area6260 Å2
MethodPISA
2
B: Nb36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7952
Polymers13,5941
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-16 kcal/mol
Surface area6260 Å2
MethodPISA
3
C: Nb36


Theoretical massNumber of molelcules
Total (without water)13,5941
Polymers13,5941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5910 Å2
MethodPISA
4
D: Nb36


Theoretical massNumber of molelcules
Total (without water)13,5941
Polymers13,5941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.610, 93.070, 142.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 22 or resid 24...
21(chain B and (resid 3 through 22 or resid 24...
31(chain C and (resid 3 through 22 or resid 24 through 95 or resid 97 through 118))
41(chain D and (resid 3 through 22 or resid 24...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 22 or resid 24...A3 - 22
121(chain A and (resid 3 through 22 or resid 24...A24 - 95
131(chain A and (resid 3 through 22 or resid 24...A97 - 102
141(chain A and (resid 3 through 22 or resid 24...A108 - 118
211(chain B and (resid 3 through 22 or resid 24...B3 - 22
221(chain B and (resid 3 through 22 or resid 24...B24 - 95
231(chain B and (resid 3 through 22 or resid 24...B97 - 102
241(chain B and (resid 3 through 22 or resid 24...B108 - 118
311(chain C and (resid 3 through 22 or resid 24 through 95 or resid 97 through 118))C3 - 22
321(chain C and (resid 3 through 22 or resid 24 through 95 or resid 97 through 118))C24 - 95
331(chain C and (resid 3 through 22 or resid 24 through 95 or resid 97 through 118))C97 - 118
411(chain D and (resid 3 through 22 or resid 24...D3 - 22
421(chain D and (resid 3 through 22 or resid 24...D24 - 95
431(chain D and (resid 3 through 22 or resid 24...D97 - 102
441(chain D and (resid 3 through 22 or resid 24...D108 - 118

-
Components

#1: Antibody
Nb36


Mass: 13594.275 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M Citric acid, 25% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.5→71.255 Å / Num. obs: 153776 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.39 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.054 / Net I/σ(I): 12.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.543.321.0751.06113320.451.2999.5
1.54-1.583.50.7881.51108540.630.93999.6
1.58-1.633.50.6331.97108540.750.7599.6
1.63-1.683.430.4872.51104770.830.57699.6
1.68-1.733.310.3653.3101950.890.4399.7
1.73-1.793.20.264.498930.930.3199.6
1.79-1.863.550.1885.894410.960.2399.5
1.86-1.943.550.1438.291480.9810.16899.5
1.94-2.023.520.10311.187280.9880.12299.5
2.02-2.123.480.08413.483840.9910.09999.5
2.12-2.233.380.06516.679690.9940.07799.4
2.23-2.373.140.05717.974710.9950.06899
2.37-2.533.570.04822.470580.9970.05799.4
2.53-2.743.510.04225.465780.9970.04999.2
2.74-33.40.03628.860300.9980.04399
3-3.353.10.03130.654190.9980.03898.3
3.35-3.873.470.02736.448240.9980.03299.2
3.87-4.743.50.02538.440670.9990.02999.4
4.74-6.73.160.02536.330930.9980.0398.1
6.7-71.2553.560.02440.317090.9990.02897.1

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.5→71.255 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.18
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 2018 2.49 %in resolution shells
Rwork0.1886 ---
obs0.1892 81007 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.34 Å2 / Biso mean: 34.5866 Å2 / Biso min: 10.9 Å2
Refinement stepCycle: final / Resolution: 1.5→71.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3459 0 2 379 3840
Biso mean--38.53 37.28 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043550
X-RAY DIFFRACTIONf_angle_d0.7814811
X-RAY DIFFRACTIONf_chiral_restr0.053545
X-RAY DIFFRACTIONf_plane_restr0.005617
X-RAY DIFFRACTIONf_dihedral_angle_d9.5542123
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2498X-RAY DIFFRACTION7.522TORSIONAL
12B2498X-RAY DIFFRACTION7.522TORSIONAL
13C2498X-RAY DIFFRACTION7.522TORSIONAL
14D2498X-RAY DIFFRACTION7.522TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.53750.291010.309755505651
1.5375-1.57910.31092020.27755355737
1.5791-1.62560.26121010.245756125713
1.6256-1.6780.26432020.221255055707
1.678-1.7380.25981010.202356245725
1.738-1.80760.21321010.190956545755
1.8076-1.88990.21072020.180555515753
1.8899-1.98950.18481010.188756485749
1.9895-2.11420.18942020.179955625764
2.1142-2.27740.20521010.17656575758
2.2774-2.50660.20482010.181456345835
2.5066-2.86940.21291010.189357315832
2.8694-3.61510.22371010.187257765877
3.6151-71.33550.20042010.178559506151
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)
10.18720.2416-0.42911.63420.29421.7385-0.0434-0.05450.01-0.01820.0421-0.012-0.18990.0777-0.00030.173-0.0084-0.0260.1766-0.00190.17826.188747.4452101.0159
20.4646-0.09130.10352.39830.4091.7788-0.0287-0.0629-0.0211-0.0672-0.00750.05110.0371-0.0582-0.00360.0810.0024-0.00120.14170.00310.1569-3.9027-19.470898.3425
31.4774-0.34210.88511.24860.44262.08330.01730.0326-0.119-0.0208-0.01750.07560.071-0.1747-00.134-0.00720.00160.2013-0.00510.1646-2.7726.78383.3553
41.0811-0.153-0.52531.9667-0.91312.3692-0.0052-0.05050.055-0.2679-0.074-0.1635-0.04590.0866-0.01760.2314-0.01210.02270.16120.00210.17257.05962.990282.6921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 119
2X-RAY DIFFRACTION2chain BB2 - 119
3X-RAY DIFFRACTION3chain CC3 - 118
4X-RAY DIFFRACTION4chain DD3 - 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