[English] 日本語
Yorodumi
- PDB-2ph1: Crystal structure of nucleotide-binding protein AF2382 from Archa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ph1
TitleCrystal structure of nucleotide-binding protein AF2382 from Archaeoglobus fulgidus, Northeast Structural Genomics Target GR165
ComponentsNucleotide-binding protein
KeywordsLIGAND BINDING PROTEIN / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


ATP-dependent FeS chaperone activity / iron-sulfur cluster assembly / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Iron-sulfur protein NUBPL-like / Mrp/NBP35 ATP-binding protein / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Iron-sulfur cluster carrier protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsForouhar, F. / Abashidze, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. ...Forouhar, F. / Abashidze, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of nucleotide-binding protein AF2382 from Archaeoglobus fulgidus.
Authors: Forouhar, F. / Abashidze, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: Nucleotide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3392
Polymers29,2741
Non-polymers651
Water66737
1
A: Nucleotide-binding protein
hetero molecules

A: Nucleotide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6784
Polymers58,5472
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1500 Å2
ΔGint-73 kcal/mol
Surface area22390 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.937, 78.186, 49.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-301-

ZN

-
Components

#1: Protein Nucleotide-binding protein


Mass: 29273.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Species: Archaeoglobus fulgidus / Strain: DSM 4304, VC-16, JCM 9628, NBRC 100126 / Gene: AF_2382 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O30288
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.49 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 7.5
Details: Protein solution: 20 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Precipitant solution: 100 mM HEPES pH 7.5, 55% MPD, MICROBATCH UNDER OIL, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→49.6 Å / Num. all: 13903 / Num. obs: 13903 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.079 / Net I/σ(I): 18.54
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 5.08 / Num. unique all: 1539 / Rsym value: 0.344 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→49.6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 112851.27 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: XtalView has also been used in the refinement. THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1211 9.7 %RANDOM
Rwork0.217 ---
all0.218 13903 --
obs0.217 12442 90.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.7637 Å2 / ksol: 0.296708 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1--15.84 Å20 Å20 Å2
2--14.77 Å20 Å2
3---1.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 1 37 1936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.357 104 9.9 %
Rwork0.271 948 -
obs-948 76.4 %

+
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