[English] 日本語
Yorodumi
- PDB-5d4o: Structure of CPII, a nitrogen regulatory PII-like protein from Th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d4o
TitleStructure of CPII, a nitrogen regulatory PII-like protein from Thiomonas intermedia K12, bound to ADP, AMP and bicarbonate.
ComponentsNitrogen regulatory protein P-II
KeywordsSIGNALING PROTEIN / carbon regulatory PII protein / CPII / nitrogen regulatory PII protein / nucleotide binding / ADP hydrolysis / bicarbonate binding / acetate binding
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / nucleotide binding
Similarity search - Function
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 / ADENOSINE MONOPHOSPHATE / BICARBONATE ION / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesThiomonas intermedia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWheatley, N.M. / Ngo, J. / Cascio, D. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein.
Authors: Wheatley, N.M. / Eden, K.D. / Ngo, J. / Rosinski, J.S. / Sawaya, M.R. / Cascio, D. / Collazo, M. / Hoveida, H. / Hubbell, W.L. / Yeates, T.O.
History
DepositionAug 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7497
Polymers35,8533
Non-polymers8964
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-24 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.440, 75.450, 80.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Nitrogen regulatory protein P-II


Mass: 11950.863 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiomonas intermedia (strain K12) (bacteria)
Strain: K12 / Gene: Tint_0114 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D5X329
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.15 M KBr, 30% (w/v) PEG MME 2000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 29590 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.42 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.055 / Χ2: 1.033 / Net I/σ(I): 19.24 / Num. measured all: 191688
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.840.840.5632.7411606216420370.61894.1
1.84-1.890.9280.4144.314329211021080.44999.9
1.89-1.950.9560.3335.4213756204020350.36199.8
1.95-2.010.9750.2467.1513409200720060.267100
2.01-2.070.9820.2058.5513044196219600.22399.9
2.07-2.150.9840.16610.2311893185418510.18199.8
2.15-2.230.990.13312.2411321183418320.14599.9
2.23-2.320.9940.1214.812001173917350.1399.8
2.32-2.420.9940.0991711531168816870.10799.9
2.42-2.540.9960.08519.4910864160916070.09399.9
2.54-2.680.9970.07621.5410050153215270.08399.7
2.68-2.840.9970.06125.328783146414580.06799.6
2.84-3.030.9970.05430.859378138913860.05999.8
3.03-3.280.9980.04536.248488128212760.04999.5
3.28-3.590.9990.03840.937525117911740.04199.6
3.59-4.010.9990.03642.576473108810830.03999.5
4.01-4.630.9990.03146.0957979629560.03399.4
4.63-5.680.9990.02948.1752988338330.032100
5.68-8.030.9990.02943.8538326536470.03299.1
8.030.9990.02450.9223103933920.02799.7

-
Processing

Software
NameVersionClassification
BUSTER-TNT2.10.0refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D4L

5d4l


Resolution: 1.8→54.9 Å / Cor.coef. Fo:Fc: 0.9467 / Cor.coef. Fo:Fc free: 0.9328 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.12 / SU Rfree Cruickshank DPI: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 1503 5.1 %RANDOM
Rwork0.2059 ---
obs0.2072 29486 99.74 %-
Displacement parametersBiso max: 117.69 Å2 / Biso mean: 35.69 Å2 / Biso min: 17.31 Å2
Baniso -1Baniso -2Baniso -3
1--2.6196 Å20 Å20 Å2
2--0.3755 Å20 Å2
3---2.2441 Å2
Refine analyzeLuzzati coordinate error obs: 0.244 Å
Refinement stepCycle: final / Resolution: 1.8→54.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 84 100 2477
Biso mean--25.17 37.06 -
Num. residues----300
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d851SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes388HARMONIC5
X-RAY DIFFRACTIONt_it2444HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion305SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2735SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2444HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3328HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion17.55
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2389 132 4.61 %
Rwork0.2244 2731 -
all0.2251 2863 -
obs--99.74 %
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)
11.3429-0.0818-0.12431.65110.62241.55920.03060.10420.1006-0.26250.0088-0.1256-0.1601-0.003-0.0394-0.0228-0.00730.0233-0.04950.0133-0.06419.7433-17.5239-28.8359
21.1821.1310.27133.39240.74231.77110.0787-0.19440.12880.4641-0.10060.09150.0034-0.02170.022-0.0418-0.01330.0072-0.02910.0021-0.083815.9917-15.7523-9.8956
31.34080.0464-0.02522.29160.31713.652-0.0343-0.0647-0.16860.19310.0070.37210.416-0.31460.0273-0.0648-0.04210.0209-0.06640.0153-0.06037.177-29.5849-19.482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 108
2X-RAY DIFFRACTION2{ B|* }B5 - 104
3X-RAY DIFFRACTION3{ C|* }C4 - 107

+
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://pdbjlvh1.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