[English] 日本語
Yorodumi
- PDB-4zr7: The structure of a domain of a functionally unknown protein from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zr7
TitleThe structure of a domain of a functionally unknown protein from Bacillus subtilis subsp. subtilis str. 168
ComponentsSensor histidine kinase ResE
KeywordsTRANSFERASE / structural genomics / PSI-Biology / protein structure initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / regulation of DNA-templated transcription / ATP binding / plasma membrane
Similarity search - Function
ResE, histidine kinase sensor domain / Histidine kinase sensor domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily ...ResE, histidine kinase sensor domain / Histidine kinase sensor domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / PAS fold / PAS fold / PAS domain / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
ACETATE ION / Sensor histidine kinase ResE
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsTan, K. / Li, H. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: To Be Published
Title: The structure of a domain of a functionally unknown protein from Bacillus subtilis subsp. subtilis str. 168
Authors: Tan, K. / Li, H. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionMay 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sensor histidine kinase ResE
B: Sensor histidine kinase ResE
C: Sensor histidine kinase ResE
D: Sensor histidine kinase ResE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,38114
Polymers57,0034
Non-polymers37810
Water3,009167
1
A: Sensor histidine kinase ResE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3574
Polymers14,2511
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sensor histidine kinase ResE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3574
Polymers14,2511
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sensor histidine kinase ResE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2862
Polymers14,2511
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sensor histidine kinase ResE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3814
Polymers14,2511
Non-polymers1303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.689, 58.689, 131.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein
Sensor histidine kinase ResE


Mass: 14250.668 Da / Num. of mol.: 4 / Fragment: UNP residues 40-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: resE, ypxE, BSU23110 / Plasmid: PMCSG68 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE)MAGIC / References: UniProt: P35164, histidine kinase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1M Lithium Chloride, 0.1M Sodium Acetate, 30% (w/v) PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.86→30 Å / Num. obs: 37320 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 34.5
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→29.345 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 1697 4.93 %random
Rwork0.171 ---
obs0.1775 34435 92.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→29.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 13 167 3850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063726
X-RAY DIFFRACTIONf_angle_d0.8865039
X-RAY DIFFRACTIONf_dihedral_angle_d15.4591376
X-RAY DIFFRACTIONf_chiral_restr0.06595
X-RAY DIFFRACTIONf_plane_restr0.003652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8591-1.91370.31451160.19951826X-RAY DIFFRACTION59
1.9137-1.97530.30611300.18562126X-RAY DIFFRACTION69
1.9753-2.04570.2827940.18582436X-RAY DIFFRACTION80
2.0457-2.12750.24321180.18912735X-RAY DIFFRACTION88
2.1275-2.2240.25041640.18282932X-RAY DIFFRACTION94
2.224-2.34090.26651320.17892952X-RAY DIFFRACTION96
2.3409-2.48690.24821490.1872936X-RAY DIFFRACTION95
2.4869-2.6780.29541900.19682964X-RAY DIFFRACTION94
2.678-2.94580.271450.18872912X-RAY DIFFRACTION95
2.9458-3.36810.22691650.17532934X-RAY DIFFRACTION94
3.3681-4.22850.20861440.14792976X-RAY DIFFRACTION95
4.2285-15.28180.20981450.15472953X-RAY DIFFRACTION94
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)
13.6431-0.2494-0.3862.25230.71412.4359-0.1744-0.20830.26950.3315-0.03660.1380.03020.1936-0.00770.1668-0.01060.03530.116-0.00410.133418.800630.8264126.2446
24.44630.17270.41292.68440.82950.85340.10.011-0.08180.202-0.07670.0183-0.07220.1056-0.09320.1761-0.0080.01860.1272-0.00340.07222.995718.5634122.8741
33.2893-0.1433-0.26851.56130.47281.02220.09390.0121-0.15190.1675-0.00580.1127-0.20760.3688-0.00340.2056-0.00810.03870.09610.03720.077412.170619.8368121.8596
42.16930.88870.11831.31920.02570.03470.0544-0.4855-0.040.3330.02380.55720.0956-0.0237-0.07060.3029-0.04760.06910.15790.00790.11857.415518.4324128.656
58.5621.7482-1.60823.7737-3.03226.8987-0.22210.66580.0916-0.44920.17220.79710.3956-0.49880.0840.2117-0.06460.00410.1468-0.01190.15670.336323.2485118.8017
63.7659-0.219-0.59223.1563-0.56012.7199-0.13990.42590.7004-0.12810.00940.2886-0.2562-0.14030.0160.2390.072-0.08590.15480.06850.26945.086532.3774118.0651
73.97325.11470.31696.58270.41010.02520.4064-0.58680.92360.74-0.42590.571-0.0648-0.29230.16140.3036-0.05710.06860.1996-0.06490.2841-2.875322.7088129.7602
84.1016-0.0657-1.25993.6041-0.10954.19990.0130.13510.3577-0.3006-0.03240.05730.20960.0534-0.01280.1537-0.05210.01580.08620.01380.150312.9628.6107120.7649
93.3674-0.3060.63923.1931-0.10820.98510.10260.09310.2431-0.16110.06480.07360.07790.0116-0.04250.11240.02710.01610.08380.02160.156110.918127.2627124.022
102.41230.9487-0.60984.14930.47221.66440.15590.07550.1192-0.1647-0.1958-0.10640.15110.0536-0.00210.09620.04720.00260.10080.01660.2112-8.90814.0445122.1548
115.2496-0.3931-0.10984.640.47933.06230.1295-0.14190.09560.09080.06960.06650.47220.0175-0.16460.1284-0.023-0.00470.13690.02270.0989-17.24089.9175125.6529
126.82594.8923-6.18678.6896-3.42625.8034-0.17210.6760.5277-0.8458-0.05660.6363-0.0351-0.80840.0940.1846-0.0069-0.05430.22750.01770.1638-21.114812.3187119.9289
133.64561.94750.90314.44980.37962.41750.2922-0.6554-0.22090.4826-0.26250.60720.0138-0.2180.17770.1499-0.03910.04040.15360.00490.264-28.99436.2969128.3384
143.76950.77340.15713.10450.75112.17120.2133-0.6184-0.54510.4703-0.29830.14040.2739-0.01460.0220.2456-0.04460.02380.11010.06580.3052-24.1295-2.7957128.9591
154.698-3.99841.99069.6809-2.49920.9470.17490.33670.2102-0.801-0.3316-0.124-0.1026-0.07160.11280.22780.04950.05140.201-0.06980.2571-32.05366.9729117.1494
163.43510.07641.13542.98571.07323.80170.0231-0.3779-0.0340.1233-0.00780.0831-0.0766-0.00820.02710.2163-0.02310.00560.1327-0.00010.0778-17.51831.8322124.6399
173.1723-0.41810.04593.9659-0.16860.77770.0935-0.07150.01460.0807-0.0565-0.3488-0.11220.0048-0.01880.0988-0.03140.02170.115-0.01080.1851-21.674728.9744124.0574
180.88210.2591-0.67084.64570.2321.1279-0.15030.34840.57-0.1592-0.3132-0.1066-0.5740.06460.37840.18080.0317-0.09520.20140.05150.4575-9.227234.8097124.6022
193.1606-0.48160.23824.08361.00077.16690.1595-0.13940.2690.4125-0.0945-0.43280.16890.31140.02050.1839-0.0372-0.0290.1236-0.07780.2329-12.611343.6367125.7913
204.1212.8883-0.43898.3963-4.33816.9471-0.0058-0.34130.1412-0.0699-0.27390.00750.3066-0.02340.34810.16180.0086-0.01640.1133-0.03390.0988-20.640535.4143127.3988
214.969-0.127-0.36714.63380.50135.19130.0883-0.3321-0.18360.15270.09230.35890.279-0.377-0.1260.1157-0.00860.02630.1008-0.04250.2424-18.932934.6939126.2248
221.905-1.15070.36768.522-4.25325.1230.00970.1294-0.5375-0.03670.0880.40640.3966-0.2203-0.15460.1410.0004-0.02420.1308-0.02690.22242.4496-7.3037126.2865
234.06132.4373-1.84227.56840.1781.520.11970.1652-0.18160.2124-0.2103-0.2069-0.1648-0.29990.01010.1330.0234-0.00540.1085-0.04090.08545.88058.1682122.9227
241.30220.046-0.08021.1334-0.66732.15460.0453-0.29680.08310.19770.0436-0.1010.18440.01370.13420.5757-0.0116-0.06990.2239-0.12880.071111.8118-1.807128.9307
257.8246-3.25945.44286.2411-2.68615.70890.49551.09530.0547-0.5359-0.336-0.16680.19710.3065-0.07390.12790.06180.0120.289-0.01290.451116.12023.2144116.0499
261.21780.3727-2.78720.1814-0.93396.48-0.1233-0.167-0.20.36710.1447-0.67680.59580.6995-0.03120.21020.0376-0.0960.2325-0.08040.592117.7352-0.933128.1762
274.8184.6155-4.0014.7069-5.0948.8857-0.4397-0.0396-0.1901-0.37390.0669-1.25470.67250.50210.24030.2497-0.0054-0.0260.21190.01920.587821.5229-7.7014118.6842
281.3982-1.21860.0261.6607-0.04751.06970.25770.3078-0.3301-0.5779-0.2433-0.0432-0.3841-0.14870.01030.57080.1012-0.03530.1753-0.01010.299212.666-13.0881116.681
296.7939-3.1971-0.64312.3098-1.76955.39810.1361-0.22110.04630.08930.23550.4487-0.60660.1664-0.40510.2554-0.0311-0.00450.15550.02160.311724.0895-16.6335130.7971
303.1058-1.44452.49343.6676-4.49975.73270.17010.403-0.0368-0.1254-0.01710.2835-0.5882-0.0779-0.05470.44640.0974-0.04380.3084-0.04990.13487.9193-3.6689117.3082
313.2127-1.38241.5233.4345-4.85857.68640.41490.1993-0.01930.0818-0.091-0.0810.70890.32-0.29420.30010.0086-0.04710.1438-0.06470.146711.1411-7.0696123.5637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 110 )
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 127 )
7X-RAY DIFFRACTION7chain 'A' and (resid 128 through 137 )
8X-RAY DIFFRACTION8chain 'A' and (resid 138 through 147 )
9X-RAY DIFFRACTION9chain 'A' and (resid 148 through 162 )
10X-RAY DIFFRACTION10chain 'B' and (resid 41 through 73 )
11X-RAY DIFFRACTION11chain 'B' and (resid 74 through 91 )
12X-RAY DIFFRACTION12chain 'B' and (resid 92 through 103 )
13X-RAY DIFFRACTION13chain 'B' and (resid 104 through 110 )
14X-RAY DIFFRACTION14chain 'B' and (resid 111 through 127 )
15X-RAY DIFFRACTION15chain 'B' and (resid 128 through 137 )
16X-RAY DIFFRACTION16chain 'B' and (resid 138 through 162 )
17X-RAY DIFFRACTION17chain 'C' and (resid 41 through 91 )
18X-RAY DIFFRACTION18chain 'C' and (resid 92 through 110 )
19X-RAY DIFFRACTION19chain 'C' and (resid 111 through 137 )
20X-RAY DIFFRACTION20chain 'C' and (resid 138 through 147 )
21X-RAY DIFFRACTION21chain 'C' and (resid 148 through 161 )
22X-RAY DIFFRACTION22chain 'D' and (resid 37 through 59 )
23X-RAY DIFFRACTION23chain 'D' and (resid 60 through 73 )
24X-RAY DIFFRACTION24chain 'D' and (resid 74 through 83 )
25X-RAY DIFFRACTION25chain 'D' and (resid 84 through 91 )
26X-RAY DIFFRACTION26chain 'D' and (resid 92 through 103 )
27X-RAY DIFFRACTION27chain 'D' and (resid 104 through 110 )
28X-RAY DIFFRACTION28chain 'D' and (resid 111 through 127 )
29X-RAY DIFFRACTION29chain 'D' and (resid 128 through 137 )
30X-RAY DIFFRACTION30chain 'D' and (resid 138 through 150 )
31X-RAY DIFFRACTION31chain 'D' and (resid 151 through 161 )

+
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