[English] 日本語
Yorodumi
- PDB-6nz1: Crystal structure of computationally designed protein XXA_GVDQ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nz1
TitleCrystal structure of computationally designed protein XXA_GVDQ
ComponentsDesign construct XXA_GVDQ
KeywordsDE NOVO PROTEIN / homotrimer / helix
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWei, K.Y. / Bick, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM124149 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Computational design of closely related proteins that adopt two well-defined but structurally divergent folds.
Authors: Wei, K.Y. / Moschidi, D. / Bick, M.J. / Nerli, S. / McShan, A.C. / Carter, L.P. / Huang, P.S. / Fletcher, D.A. / Sgourakis, N.G. / Boyken, S.E. / Baker, D.
History
DepositionFeb 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Design construct XXA_GVDQ
B: Design construct XXA_GVDQ
C: Design construct XXA_GVDQ
D: Design construct XXA_GVDQ
E: Design construct XXA_GVDQ
F: Design construct XXA_GVDQ


Theoretical massNumber of molelcules
Total (without water)67,2306
Polymers67,2306
Non-polymers00
Water4,630257
1
A: Design construct XXA_GVDQ
B: Design construct XXA_GVDQ
C: Design construct XXA_GVDQ


Theoretical massNumber of molelcules
Total (without water)33,6153
Polymers33,6153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-91 kcal/mol
Surface area13320 Å2
MethodPISA
2
D: Design construct XXA_GVDQ
E: Design construct XXA_GVDQ
F: Design construct XXA_GVDQ


Theoretical massNumber of molelcules
Total (without water)33,6153
Polymers33,6153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-90 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.647, 76.747, 91.946
Angle α, β, γ (deg.)90.000, 106.060, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Design construct XXA_GVDQ


Mass: 11204.926 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.03 M of each divalent cation (magnesium chloride, calcium chloride), 0.1 M MES/imidazole pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1111 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1111 Å / Relative weight: 1
ReflectionResolution: 1.74→88.36 Å / Num. obs: 68147 / % possible obs: 98.68 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.074 / Rrim(I) all: 0.19 / Net I/σ(I): 6.2
Reflection shellResolution: 1.74→1.81 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 6108 / CC1/2: 0.336 / % possible all: 89.18

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rosetta model

Resolution: 1.9→88.356 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.06 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2159 1567 2.94 %
Rwork0.1847 51644 -
obs0.1925 53261 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.77 Å2 / Biso mean: 31.5168 Å2 / Biso min: 15.34 Å2
Refinement stepCycle: final / Resolution: 1.9→88.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4299 0 0 257 4556
Biso mean---33.13 -
Num. residues----569
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9007-1.9620.36811500.33434705485597
1.962-2.03210.2881400.29594679481997
2.0321-2.11350.31311380.26874664480297
2.1135-2.20970.26381440.24674674481897
2.2097-2.32620.25821380.2194654479297
2.3262-2.47190.26171440.19254673481797
2.4719-2.66280.21261440.19274708485297
2.6628-2.93080.23181370.18164679481697
2.9308-3.35480.18821380.18274705484397
3.3548-4.22650.17161440.14714726487097
4.2265-57.96790.19861460.16224777492396
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)
10.00270.0008-0.00010.0006-0.00080.0015-0.00060.0212-0.0162-0.0068-0.0003-0.00340.0080.00390.00020.34260.001-0.02950.4974-0.02940.137738.44425.95637.028
20.0035-0.00020.0080.0392-0.00340.0217-0.0082-0.0182-0.0181-0.02470.01840.01320.0044-0.00960.00950.11960.0031-0.00630.3770.00420.084728.17529.79159.135
30.0001-0.0002-0.00060.00510.01160.0260.00350.01980.0030.01470.00050.006-0.0039-0.00940.00220.1166-0.0036-0.00240.3592-0.00960.084529.2739.54377.899
40.00840.00230.0050.00250.00050.0163-0.0017-0.010.0015-0.00480.00860.0037-0.0015-0.00710.00740.1298-0.01120.00020.40820.02080.100521.80336.42343.254
50.0087-0.0051-0.0130.01910.00710.01970.00450.00390.0088-0.0044-0.0046-0.0013-0.00420.0023-0.04050.1055-0.0020.00420.39280.02040.08733.237.95859.106
60.00130.0011-0.00310.0015-0.00330.0086-0.00650.01250.00250.00260.0087-0.0045-0.00320.009-0.00120.1045-0.0007-0.010.30550.02140.076544.13728.22776.921
70.00120.00280.00030.00740.0010.0002-0.00350.00180.0027-0.02790.0066-0.0026-0.00750.01740.00080.18020.0011-0.01270.38410.00840.093239.89243.61544.596
80.0111-0.0009-0.0040.02660.01050.0065-0.00590.01720.0025-0.02360.0154-0.0032-0.00810.00840.05320.1212-0.01580.0030.4168-0.00270.092537.49929.77657.664
90.0055-0.004-0.00090.00370.00070.00020.0029-0.00230.00220.0120.00880.01820.0058-0.01090.00190.2536-0.02260.04230.42340.03480.165124.74721.00278.86
100.0144-0.00310.00910.0019-0.00760.0329-0.005-0.0152-0.00330.01340.0061-0.00570.00650.0132-0.00450.2399-0.0062-0.02520.3755-0.030.098913.49649.85797.43
110.0140.0028-0.00110.02020.00530.0018-0.00090.00850.00510.00410.00490.0016-0.0013-0.01720.05160.10790.00820.00490.39260.00480.08253.30943.10269.876
120.0219-0.00630.00930.00610.00150.0191-0.00430.0152-0.00330.00390.01010.0065-0.0005-0.01230.00580.1304-0.00880.00380.33940.00360.0821-3.35439.97692.702
130.01790.00720.00880.0117-0.0010.0170.01090.00610.00310.0004-0.0201-0.0030.00210.0026-0.03710.0946-0.004-0.00250.36880.03060.08397.71738.51576.904
140.0001-0.0001-0.0001-0-0-00-0.00960.0019-0.00910.0055-0.0071-0.00480.0148-0.00840.13250.00270.01650.34940.04260.097419.16948.21759.088
150.01370.0025-0.00990.03270.02090.0233-0.0050.00190.00530.041-0.0183-0.00590.0144-0.0045-0.0220.18770.0085-0.0120.41210.00560.101414.34632.49891.516
160.01330.00660.00260.010.00450.002-0.0046-0.0328-0.00450.04270.011-0.00490.01180.00960.020.13960.0087-0.00140.3733-0.00920.083712.34346.49978.194
170.00230.000200000.00690.00660.0067-0.0061-0.0010.012-0.0049-0.0047-00.30470.03820.00240.43510.07560.2261-0.1555.37956.634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:23 )A5 - 23
2X-RAY DIFFRACTION2( CHAIN A AND RESID 24:69 )A24 - 69
3X-RAY DIFFRACTION3( CHAIN A AND RESID 70:93 )A70 - 93
4X-RAY DIFFRACTION4( CHAIN B AND RESID 0:23 )B0 - 23
5X-RAY DIFFRACTION5( CHAIN B AND RESID 24:68 )B24 - 68
6X-RAY DIFFRACTION6( CHAIN B AND RESID 69:93 )B69 - 93
7X-RAY DIFFRACTION7( CHAIN C AND RESID 0:23 )C0 - 23
8X-RAY DIFFRACTION8( CHAIN C AND RESID 24:68 )C24 - 68
9X-RAY DIFFRACTION9( CHAIN C AND RESID 69:90 )C69 - 90
10X-RAY DIFFRACTION10( CHAIN D AND RESID 3:23 )D3 - 23
11X-RAY DIFFRACTION11( CHAIN D AND RESID 24:93 )D24 - 93
12X-RAY DIFFRACTION12( CHAIN E AND RESID 0:23 )E0 - 23
13X-RAY DIFFRACTION13( CHAIN E AND RESID 24:68 )E24 - 68
14X-RAY DIFFRACTION14( CHAIN E AND RESID 69:93 )E69 - 93
15X-RAY DIFFRACTION15( CHAIN F AND RESID -1:23 )F-1 - 23
16X-RAY DIFFRACTION16( CHAIN F AND RESID 24:68 )F24 - 68
17X-RAY DIFFRACTION17( CHAIN F AND RESID 69:90 )F69 - 90

+
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