[English] 日本語
Yorodumi
- PDB-4fdk: F78L Tt H-NOX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fdk
TitleF78L Tt H-NOX
ComponentsMethyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins
KeywordsSIGNALING PROTEIN / O2-sensor
Function / homology
Function and homology information


lysozyme activity / heme binding / signal transduction / membrane / metal ion binding
Similarity search - Function
H-NOX domain / H-NOX domain / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). ...H-NOX domain / H-NOX domain / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWeinert, E.E. / Phillips-Piro, C.M. / Marletta, M.A.
CitationJournal: J.Inorg.Biochem. / Year: 2013
Title: Porphyrin pi-stacking in a heme protein scaffold tunes gas ligand affinity.
Authors: Weinert, E.E. / Phillips-Piro, C.M. / Marletta, M.A.
History
DepositionMay 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3246
Polymers44,0272
Non-polymers1,2974
Water5,044280
1
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6623
Polymers22,0131
Non-polymers6482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6623
Polymers22,0131
Non-polymers6482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.552, 127.426, 42.935
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis proteins / H-NOX protein


Mass: 22013.484 Da / Num. of mol.: 2 / Fragment: UNP residues 1-188 / Mutation: F78L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: Tar4, TTE0680 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RBX6
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.4
Details: 0.2 M sodium citrate, pH 4.4, 25% w/v PEG3350, 25 mg/mL protein in 20 mM TEA, pH 7.5, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2010
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 26664 / Num. obs: 26525 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.414 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
PHASERphasing
ELVESrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U55 CHAIN A

1u55


Resolution: 2.1→49.971 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 1334 5.03 %RANDOM
Rwork0.1696 ---
obs0.1728 26525 99.67 %-
all-26664 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.239 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.9025 Å20 Å2-0 Å2
2--7.6214 Å20 Å2
3----0.7189 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 90 280 3466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143289
X-RAY DIFFRACTIONf_angle_d1.3924447
X-RAY DIFFRACTIONf_dihedral_angle_d16.61261
X-RAY DIFFRACTIONf_chiral_restr0.08457
X-RAY DIFFRACTIONf_plane_restr0.007558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.32951180.232512X-RAY DIFFRACTION100
2.1751-2.26220.24551260.18682471X-RAY DIFFRACTION100
2.2622-2.36510.20121470.17472463X-RAY DIFFRACTION100
2.3651-2.48980.32221280.18262483X-RAY DIFFRACTION100
2.4898-2.64580.26651290.18862498X-RAY DIFFRACTION100
2.6458-2.85010.25871310.18272534X-RAY DIFFRACTION100
2.8501-3.13680.24981430.16942489X-RAY DIFFRACTION100
3.1368-3.59060.22651380.16772529X-RAY DIFFRACTION100
3.5906-4.52340.21131300.14142546X-RAY DIFFRACTION99
4.5234-49.98530.20611440.17272666X-RAY DIFFRACTION99
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)
10.0972-0.0434-0.11250.0120.04540.1167-0.1464-0.252-0.1295-0.14950.096-0.1049-0.2558-0.1096-0.00040.27460.00260.07120.2691-0.04220.278512.217220.601419.8427
20.0083-0.0066-0.00980.03110.03110.0315-0.1485-0.4913-0.03880.04560.22130.1181-0.114-0.1887-0.00030.33210.01330.05290.3756-0.00450.2443.063117.912227.663
30.4620.1767-0.18220.10790.00830.20170.319-0.54181.18930.2160.1940.0249-0.2997-0.22460.00680.4649-0.04290.12580.413-0.070.527612.606126.976428.5228
40.9607-0.03150.18160.10750.04720.2307-0.2474-0.3895-0.87060.50360.0175-0.02550.41570.2461-0.01050.3696-0.01660.10190.3850.07970.347711.098111.565728.0017
50.2004-0.0325-0.1250.01820.02740.0808-0.03830.1562-0.2152-0.11210.13010.12720.1003-0.02300.23130.00190.08730.25230.01690.289213.883615.598414.3814
60.06130.01910.00710.0498-0.03880.03560.0721-0.14460.0383-0.3674-0.25990.1072-0.15180.04590.00030.5375-0.09660.03210.36970.02570.286321.415826.58084.8509
70.261-0.2929-0.05060.32440.05220.0082-0.02210.27110.1818-0.24870.0497-0.7492-0.07560.3559-0.04270.3408-0.02710.11670.2367-0.02550.351128.872322.843710.6884
80.46980.0744-0.24860.50090.08220.162-0.2765-0.2478-0.21130.45350.0685-0.51390.11180.1498-0.05130.32510.0213-0.04320.267-0.04080.22431.264424.494821.9761
90.1106-0.1570.04350.4005-0.00310.0433-0.2190.0526-0.55230.05490.1509-0.41330.21020.0496-0.07270.3018-0.02340.17360.2917-0.02750.356931.558411.76611.9429
100.0839-0.11390.15710.6761-0.12960.5457-0.1380.0852-0.3022-0.0059-0.25710.0495-0.0794-0.2655-0.15840.2737-0.01880.1230.301-0.05140.248120.058813.080210.1246
110.76750.083-0.43750.1362-0.00320.2705-0.33120.2487-0.49530.07140.0523-0.3981-0.1228-0.2766-0.1230.32150.01870.09830.2642-0.07730.486127.15056.09369.9839
120.1980.1042-0.11080.1849-0.04430.05960.074-0.1674-0.01680.1655-0.0018-0.63650.08350.37970.00440.3369-0.02430.04070.2912-0.0350.462131.83848.52313.0705
130.0053-0.03980.04290.3736-0.40360.43210.1032-0.06560.3268-0.07450.322-0.1672-0.4504-0.10171.08090.4944-0.51460.67910.7549-0.23420.480637.524915.3298-5.2422
140.1885-0.0997-0.16780.1060.01410.1895-0.2314-0.57090.04570.22540.12380.10660.29630.4989-0.00060.35880.0711-0.04990.3418-0.02740.25433.1345.165830.9814
150.07970.075-0.00270.06880.01570.0453-0.1447-0.2908-0.30580.54460.0435-0.13290.78430.58460.00020.82460.05910.12150.75550.03120.428928.649138.891338.1457
160.6943-0.07060.1660.9074-0.48070.2806-0.2754-0.50050.65850.92260.2797-0.3619-0.4308-0.18880.05450.4770.061-0.11260.4654-0.15060.429331.088953.735535.5649
170.4567-0.205-0.30260.3019-0.0620.3323-0.17240.2071-0.0407-0.0306-0.12770.06480.0749-0.1444-0.00870.23520.0047-0.00830.2267-0.10220.317125.266944.813919.8799
180.47620.0246-0.00040.58360.26220.11750.0163-0.0106-0.5721-0.0775-0.24770.72890.235-0.4782-0.09650.2622-0.036-0.01480.2805-0.05660.505912.295341.4719.927
190.9699-0.2581-0.65590.8740.89761.1138-0.3993-0.1359-0.34180.1604-0.04560.6230.6476-0.439-0.48440.3726-0.00470.06780.3662-0.04730.43269.034145.294225.1326
200.3926-0.2771-0.02570.3767-0.06620.0705-0.24940.24630.1271-0.064-0.07820.32740.01140.0486-0.00510.26280.0141-0.0530.2961-0.04270.265317.129252.104819.7128
210.43370.07320.07150.573-0.06420.0224-0.0727-0.07150.0431-0.1382-0.19020.51550.05780.2187-0.02510.36280.1102-0.03370.43910.00740.315313.017257.561418.8105
220.18950.0088-0.09750.8138-0.13620.07390.07250.0393-0.091-0.07950.10550.10420.15620.55620.10340.62910.362-0.25921.0065-0.16090.44484.74748.24832.6597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:17)
2X-RAY DIFFRACTION2chain 'A' and (resseq 18:29)
3X-RAY DIFFRACTION3chain 'A' and (resseq 30:44)
4X-RAY DIFFRACTION4chain 'A' and (resseq 45:62)
5X-RAY DIFFRACTION5chain 'A' and (resseq 63:81)
6X-RAY DIFFRACTION6chain 'A' and (resseq 82:90)
7X-RAY DIFFRACTION7chain 'A' and (resseq 91:106)
8X-RAY DIFFRACTION8chain 'A' and (resseq 107:118)
9X-RAY DIFFRACTION9chain 'A' and (resseq 119:137)
10X-RAY DIFFRACTION10chain 'A' and (resseq 138:152)
11X-RAY DIFFRACTION11chain 'A' and (resseq 153:166)
12X-RAY DIFFRACTION12chain 'A' and (resseq 167:178)
13X-RAY DIFFRACTION13chain 'A' and (resseq 179:188)
14X-RAY DIFFRACTION14chain 'B' and (resseq 1:28)
15X-RAY DIFFRACTION15chain 'B' and (resseq 29:44)
16X-RAY DIFFRACTION16chain 'B' and (resseq 45:62)
17X-RAY DIFFRACTION17chain 'B' and (resseq 63:90)
18X-RAY DIFFRACTION18chain 'B' and (resseq 91:107)
19X-RAY DIFFRACTION19chain 'B' and (resseq 108:123)
20X-RAY DIFFRACTION20chain 'B' and (resseq 124:152)
21X-RAY DIFFRACTION21chain 'B' and (resseq 153:178)
22X-RAY DIFFRACTION22chain 'B' and (resseq 179:188)

+
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