[English] 日本語
Yorodumi
- PDB-2xzw: STRUCTURE OF PII FROM SYNECHOCOCCUS ELONGATUS IN COMPLEX WITH 2- ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xzw
TitleSTRUCTURE OF PII FROM SYNECHOCOCCUS ELONGATUS IN COMPLEX WITH 2- OXOGLUTARATE AT LOW 2-OG CONCENTRATIONS
ComponentsNITROGEN REGULATORY PROTEIN P-II
KeywordsSIGNALING PROTEIN
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
2-OXOGLUTARIC ACID / ADENOSINE-5'-TRIPHOSPHATE / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZeth, K. / Chellamuthu, V.-R. / Forchhammer, K. / Fokina, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Mechanism of 2-Oxoglutarate Signaling by the Synechococcus Elongatus Pii Signal Transduction Protein.
Authors: Fokina, O. / Chellamuthu, V.-R. / Forchhammer, K. / Zeth, K.
History
DepositionNov 29, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionDec 8, 2010ID: 2XUN
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_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_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_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
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
G: NITROGEN REGULATORY PROTEIN P-II
H: NITROGEN REGULATORY PROTEIN P-II
I: NITROGEN REGULATORY PROTEIN P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,37030
Polymers114,7839
Non-polymers5,58721
Water5,729318
1
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)40,29412
Polymers38,2613
Non-polymers2,0339
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11860 Å2
ΔGint-75.3 kcal/mol
Surface area13540 Å2
MethodPISA
2
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)39,9538
Polymers38,2613
Non-polymers1,6925
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-56.8 kcal/mol
Surface area12470 Å2
MethodPISA
3
G: NITROGEN REGULATORY PROTEIN P-II
H: NITROGEN REGULATORY PROTEIN P-II
I: NITROGEN REGULATORY PROTEIN P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,12310
Polymers38,2613
Non-polymers1,8627
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-60.2 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.334, 102.370, 135.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 110
2114B1 - 110
3114C1 - 110
4114D1 - 110
5114E1 - 110
6114F1 - 110
7114G1 - 110
8114H1 - 110
9114I1 - 110

-
Components

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


Mass: 12753.712 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A3F4
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.19 Å3/Da / Density % sol: 43.83 % / Description: NONE

-
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: 1.95→48 Å / Num. obs: 69753 / % possible obs: 98.1 % / Observed criterion σ(I): 1.8 / Redundancy: 7.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.8 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XBP

2xbp


Resolution: 1.95→47.89 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.666 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22513 3672 5 %RANDOM
Rwork0.17537 ---
obs0.17785 69752 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.433 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7394 0 345 318 8057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0227850
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1962.02710607
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3615962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79224.708308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.522151494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9591560
X-RAY DIFFRACTIONr_chiral_restr0.1480.21266
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025503
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2691.54769
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24327727
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.89933081
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.3644.52872
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 704 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.570.5
2Bmedium positional0.430.5
3Cmedium positional0.450.5
4Dmedium positional0.520.5
5Emedium positional1.030.5
6Fmedium positional0.440.5
7Gmedium positional1.080.5
8Hmedium positional0.60.5
9Imedium positional0.910.5
1Amedium thermal1.772
2Bmedium thermal1.882
3Cmedium thermal1.972
4Dmedium thermal2.192
5Emedium thermal2.32
6Fmedium thermal1.842
7Gmedium thermal2.52
8Hmedium thermal2.192
9Imedium thermal2.132
LS refinement shellResolution: 1.946→1.996 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 246 -
Rwork0.228 4674 -
obs--100 %
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)
10.9331-0.6484-0.191.06820.25860.4192-0.0474-0.1538-0.13130.13930.00210.10410.04150.00760.04530.0316-0.00730.02580.05640.01580.0613-12.584-6.289-18.2
20.4123-0.0368-0.08970.609-0.16810.631-0.02090.0006-0.06110.0180.00640.0135-0.01520.05250.01450.0061-0.0140.01020.0562-0.00130.0496-3.372-6.663-35.356
30.456-0.3271-0.42980.24270.26270.7222-0.0232-0.00010.04240.02950.0048-0.034-0.05140.00730.01840.0327-0.01240.01050.0575-0.01240.063-14.4578.291-28.316
40.59230.1095-0.23521.1331-0.34950.59470.04360.02940.05940.0614-0.0097-0.032-0.05860.0076-0.03390.02850.00110.02730.0516-0.00840.0386-48.28812.129-55.138
50.2664-0.2540.44840.3137-0.30131.7091-0.0399-0.02830.06290.03560.0254-0.03290.0074-0.03670.01450.0467-0.00410.0060.0566-0.01270.0816-38.77215.018-38.805
61.0410.18040.38450.28960.17260.3765-0.006-0.0295-0.09930.01980.0061-0.02150.06570.003600.0266-0.00170.02090.07010.00190.0417-49.599-1.347-42.933
71.9558-0.21780.19050.4108-0.06390.849-0.0146-0.08780.16650.08780.0457-0.0734-0.16280.1311-0.0310.0581-0.0223-0.00620.0467-0.01320.053-20.7934.577-71.03
80.604-0.2568-0.0850.6619-0.11120.47790.0372-0.0640.03880.0642-0.0212-0.07490.0010.1331-0.01610.0316-0.0048-0.00730.0708-0.01180.0274-13.31416.287-76.567
90.9019-0.4027-0.4590.56490.08760.41770.02120.0590.0012-0.00210.02050.0430.0012-0.0396-0.04180.0268-0.0044-0.00050.05330.00640.0168-31.60720.762-76.027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 112
2X-RAY DIFFRACTION2B3 - 112
3X-RAY DIFFRACTION3C3 - 112
4X-RAY DIFFRACTION4D3 - 112
5X-RAY DIFFRACTION5E3 - 112
6X-RAY DIFFRACTION6F3 - 112
7X-RAY DIFFRACTION7G3 - 112
8X-RAY DIFFRACTION8H3 - 112
9X-RAY DIFFRACTION9I3 - 112

+
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