[English] 日本語
Yorodumi
- PDB-4c3k: Structure of mixed PII-ADP complexes from S. elongatus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c3k
TitleStructure of mixed PII-ADP complexes from S. elongatus
ComponentsNITROGEN REGULATORY PROTEIN P-II
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / nucleotide binding / identical protein binding
Similarity search - Function
Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta ...Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.099 Å
AuthorsZeth, K. / Forchhammer, K.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis and Target-Specific Modulation of Adp Sensing by the Synechococcus Elongatus Pii Signaling Protein.
Authors: Zeth, K. / Fokina, O. / Forchhammer, K.
History
DepositionAug 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Apr 16, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _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: NITROGEN REGULATORY PROTEIN P-II
B: NITROGEN REGULATORY PROTEIN P-II
C: NITROGEN REGULATORY PROTEIN P-II
D: NITROGEN REGULATORY PROTEIN P-II
E: NITROGEN REGULATORY PROTEIN P-II
F: NITROGEN REGULATORY PROTEIN P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,32611
Polymers76,5226
Non-polymers1,8045
Water0
1
D: NITROGEN REGULATORY PROTEIN P-II
E: NITROGEN REGULATORY PROTEIN P-II
F: NITROGEN REGULATORY PROTEIN P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5436
Polymers38,2613
Non-polymers1,2823
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-45.4 kcal/mol
Surface area12380 Å2
MethodPISA
2
A: NITROGEN REGULATORY PROTEIN P-II
B: NITROGEN REGULATORY PROTEIN P-II
C: NITROGEN REGULATORY PROTEIN P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7835
Polymers38,2613
Non-polymers5222
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-44.2 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.463, 122.463, 80.476
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein
NITROGEN REGULATORY PROTEIN P-II / PII SIGNAL TRANSDUCING PROTEIN / PII


Mass: 12753.712 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A3F4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7.5 / Details: 20% PEG4000, 100 MM TRIS, PH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→45 Å / Num. obs: 11089 / % possible obs: 87.8 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.8
Reflection shellResolution: 3.1→3.29 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.8 / % possible all: 90

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AFF

4aff


Resolution: 3.099→48.73 Å / SU ML: 0.41 / σ(F): 1.99 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2694 555 5 %
Rwork0.2142 --
obs0.2169 11090 87.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.099→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4413 0 113 0 4526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044555
X-RAY DIFFRACTIONf_angle_d1.0386151
X-RAY DIFFRACTIONf_dihedral_angle_d14.0361707
X-RAY DIFFRACTIONf_chiral_restr0.049768
X-RAY DIFFRACTIONf_plane_restr0.005760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0988-3.41050.36141420.30392691X-RAY DIFFRACTION90
3.4105-3.90390.31231400.24112683X-RAY DIFFRACTION90
3.9039-4.91770.23031390.17552641X-RAY DIFFRACTION88
4.9177-48.73590.23391340.19432520X-RAY DIFFRACTION83
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)
14.25432.1473-0.2424.44490.25131.1974-0.0274-0.29-0.3290.02290.2404-0.3219-0.1336-0.2305-0.1240.2755-0.1034-0.14820.50710.06970.2633-22.243418.7722.1558
27.24552.532-1.03461.67020.40225.28480.50860.36551.2952-0.07640.70312.34560.7024-0.3849-1.02030.699-0.0648-0.15050.56940.16311.1834-40.595617.43956.8239
36.8983.8857-7.79142.6994-4.33599.72540.57450.7138-0.61360.0266-0.91180.0462-0.88630.21370.07080.2519-0.0366-0.03070.52780.02950.4158-22.520823.4438-3.0806
47.87671.0145-0.42359.3043-3.68631.57420.04270.6714-0.1073-0.8768-0.0578-0.1595-0.39060.26080.23950.4459-0.0889-0.02380.3581-0.04450.2346-21.015714.7473-6.6107
52.49661.1980.06031.39940.52270.2917-0.0690.65020.6172-0.29760.20070.4705-0.0195-0.1285-0.03490.45850.0017-0.00660.49810.15680.3586-23.2425.5727-3.1084
68.2161-6.3428-1.85016.07932.40651.2267-0.6477-0.38630.6267-0.32190.6649-0.6516-0.80730.4356-0.16821.1492-0.3562-0.06260.4946-0.00470.1918-10.32831.2915-3.5393
74.70270.9355-0.12052.38452.18844.6143-0.06870.07630.579-0.32510.36560.82550.7561-0.6568-0.52950.6423-0.1952-0.24240.53510.40631.1365-46.358628.21210.4605
85.46420.15920.38272.58961.33885.30170.26461.05890.5005-0.2750.37510.74850.2979-0.0164-0.62210.46710.0631-0.06630.71180.42791.0625-42.664729.5927-1.002
92.1206-0.8215-0.98934.8567-1.51414.0975-0.10670.40120.4370.23910.07150.25430.0586-0.4831-0.04190.5679-0.0458-0.16460.87580.11480.3656-37.947226.7955-5.4999
102.408-2.9428-0.38723.7502-0.27245.24170.120.0641.6319-0.40970.3220.3382-0.22230.5528-0.1680.4257-0.06860.14040.1530.26020.9376-25.626742.44456.8408
115.63683.6137-5.45963.9188-2.2782.02720.74360.8856-0.19390.76480.30290.322-0.9469-1.0856-0.08420.44750.0381-0.01390.616-0.25180.6333-30.214336.68237.5933
125.8844-4.46354.83457.22720.43168.43650.3763-2.1797-1.84370.34730.7235-0.5842-0.46060.3727-0.96450.5813-0.0378-0.14141.06450.09760.692-14.078723.187612.8043
138.09270.92341.13646.4303-1.72887.0052-0.00770.22121.59030.23250.6471.1511-0.5658-1.2571-0.4860.43530.00970.17440.47030.1140.6593-24.726742.13111.6395
141.3552-0.5129-0.24631.9038-1.23352.09470.39260.10780.75930.74820.35871.0656-1.3822-0.39480.07350.01170.4512-0.09850.67580.5120.7956-29.85939.208-1.026
152.16443.4942-2.38187.4551-5.52376.03710.3060.00910.15260.32770.84120.96350.6381-0.4805-1.19610.3946-0.05050.20340.5576-0.14210.5673-26.257722.3576-32.3539
162.47574.4503-2.04588.7043-2.88694.2427-0.74830.0216-0.7352-0.98370.5469-2.06840.7927-0.32810.01110.5934-0.07470.18560.4108-0.0940.3889-16.9816.8132-39.5745
176.0232-4.86994.30974.5328-4.67865.79610.56150.47121.4023-1.2618-1.4408-1.17920.6439-0.16240.51740.36060.04070.16880.62720.05620.4937-26.861521.2019-40.3079
181.95971.6328-1.47179.98213.46063.64691.5404-0.14412.8995-0.06650.94830.3275-1.5221.2752-2.25640.9326-0.23990.6510.70270.07491.9744-23.484340.1131-38.5052
198.26330.13690.34016.1858-0.79616.0427-0.0088-0.76060.1010.90120.2544-0.1139-0.8318-0.1139-0.13180.5153-0.08770.28610.3884-0.11430.2783-22.70219.4568-31.8153
203.83494.9749-3.01126.6209-3.30454.28720.3326-2.64540.13750.6762-0.82360.19971.76481.71660.59120.79970.1552-0.00280.7248-0.1270.485-13.587330.3685-33.9994
211.76791.99870.9776.93753.16761.434-0.1866-0.2535-0.27240.82670.2331-0.25190.48670.2215-0.07840.7454-0.0030.07530.4447-0.01110.3708-35.404710.7899-31.5885
223.12281.7355-0.77015.5816-3.3014.51750.6150.23111.5457-0.4098-0.6467-0.15-0.04630.3435-0.30190.55140.0160.28620.5511-0.08611.2603-35.311840.7776-35.5994
233.1211-0.96990.93956.98042.34815.68490.66440.50690.3683-0.7308-0.12160.1169-0.6010.3962-0.50070.76150.00570.26650.52470.16620.7511-38.646233.0858-42.4078
242.16390.51680.30931.4042-0.7270.50170.3609-0.67740.56890.359-0.17730.3446-0.35890.2838-0.20740.87950.14240.68620.52860.03391.0135-36.487639.3767-29.4999
255.40460.0188-0.51222.2777-0.621.9156-0.16330.22531.72290.7379-0.2910.6748-0.5940.0908-0.11140.8212-0.10540.29960.5546-0.16690.829-31.617833.0338-29.3869
263.6615-0.2189-1.58582.16621.63083.87780.10831.22720.7294-0.11790.09621.49710.4895-0.77320.1290.29630.63240.31770.41380.00590.6765-45.490118.0323-42.2974
273.23910.6445-0.25311.0331-0.45342.279-0.0446-0.7492-0.30830.56480.80231.4312-0.4645-1.0766-0.81380.71240.40640.31440.83340.54881.2744-53.530523.1588-40.0011
286.6599-0.82831.73694.79980.821.57060.83980.4962-0.1718-1.283-0.1492-0.74970.070.7869-0.5880.60780.02750.16440.4899-0.03420.3431-29.69215.213-46.856
294.45761.8751-1.99073.0352-0.99077.2824-0.2756-0.72760.54210.95950.25151.1930.0671-0.34280.21590.6938-0.01780.25270.42110.1350.5674-42.642620.8417-37.4486
302.53941.12361.36973.18630.19621.3956-0.4540.0048-0.4590.91330.26661.01410.9202-0.12490.56570.7188-0.15960.33660.47670.06730.6303-44.274212.3868-37.2312
312.20692.45021.18022.94142.12984.9599-0.77820.992-0.2039-0.88040.42291.0214-1.02540.0957-1.00331.05510.05031.53350.81191.00250.9141-47.610336.6432-29.783
326.17661.76023.40540.87851.03782.93220.1811-0.47050.61251.6472.9712-1.80950.95652.4019-2.89921.25340.21280.27921.8424-0.44793.0398-53.513131.6421-30.131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 33 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 34 THROUGH 57 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 58 THROUGH 69 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 70 THROUGH 81 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 82 THROUGH 107 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 108 THROUGH 116 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 1 THROUGH 23 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 24 THROUGH 81 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 82 THROUGH 108 )
10X-RAY DIFFRACTION10CHAIN C AND (RESID 1 THROUGH 23 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 24 THROUGH 35 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 36 THROUGH 55 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 56 THROUGH 81 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 82 THROUGH 108 )
15X-RAY DIFFRACTION15CHAIN D AND (RESID 1 THROUGH 9 )
16X-RAY DIFFRACTION16CHAIN D AND (RESID 10 THROUGH 23 )
17X-RAY DIFFRACTION17CHAIN D AND (RESID 24 THROUGH 35 )
18X-RAY DIFFRACTION18CHAIN D AND (RESID 36 THROUGH 55 )
19X-RAY DIFFRACTION19CHAIN D AND (RESID 56 THROUGH 81 )
20X-RAY DIFFRACTION20CHAIN D AND (RESID 82 THROUGH 90 )
21X-RAY DIFFRACTION21CHAIN D AND (RESID 91 THROUGH 115 )
22X-RAY DIFFRACTION22CHAIN E AND (RESID 1 THROUGH 23 )
23X-RAY DIFFRACTION23CHAIN E AND (RESID 24 THROUGH 57 )
24X-RAY DIFFRACTION24CHAIN E AND (RESID 58 THROUGH 81 )
25X-RAY DIFFRACTION25CHAIN E AND (RESID 82 THROUGH 111 )
26X-RAY DIFFRACTION26CHAIN F AND (RESID 1 THROUGH 21 )
27X-RAY DIFFRACTION27CHAIN F AND (RESID 22 THROUGH 28 )
28X-RAY DIFFRACTION28CHAIN F AND (RESID 29 THROUGH 55 )
29X-RAY DIFFRACTION29CHAIN F AND (RESID 56 THROUGH 68 )
30X-RAY DIFFRACTION30CHAIN F AND (RESID 69 THROUGH 95 )
31X-RAY DIFFRACTION31CHAIN F AND (RESID 96 THROUGH 107 )
32X-RAY DIFFRACTION32CHAIN F AND (RESID 108 THROUGH 114 )

+
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