[English] 日本語
Yorodumi
- PDB-2nvm: Crystal structure of fdxN element excision controlling factor Xis... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nvm
TitleCrystal structure of fdxN element excision controlling factor XisI (YP_321976.1) from Anabaena Variabilis ATCC 29413 at 2.19 A resolution
ComponentsFdxN element excision controlling factor XisI
KeywordsStructural Genomics/Unknown Function / YP_321976.1 / fdxN element excision controlling factor XisI / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / Structural Genomics-Unknown Function COMPLEX
Function / homologyXisI-like / XisI protein / XisI-like superfamily / XisI protein / TATA-Binding Protein / 2-Layer Sandwich / Alpha Beta / FdxN element excision controlling factor XisI
Function and homology information
Biological speciesAnabaena variabilis ATCC 29413 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.19 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2014
Title: Site-specific recombination of nitrogen-fixation genes in cyanobacteria by XisF-XisH-XisI complex: Structures and models.
Authors: Hwang, W.C. / Golden, J.W. / Pascual, J. / Xu, D. / Cheltsov, A. / Godzik, A.
History
DepositionNov 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Sep 10, 2014Group: Database references
Revision 1.4Sep 24, 2014Group: Database references
Revision 1.5Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.6Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.7Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FdxN element excision controlling factor XisI
B: FdxN element excision controlling factor XisI


Theoretical massNumber of molelcules
Total (without water)29,1872
Polymers29,1872
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-4 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.440, 122.440, 77.076
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 6 / Auth seq-ID: 3 - 117 / Label seq-ID: 4 - 118

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein FdxN element excision controlling factor XisI


Mass: 14593.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria)
Species: Anabaena variabilis / Strain: ATCC 29413 / PCC 7937 / Gene: YP_321976.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3MD55
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6
Details: 30.0% PEG-6000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0000, 0.9795, 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2006
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
30.97921
ReflectionResolution: 2.1→62.38 Å / Num. obs: 18064 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 49.03 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.19-2.3110.71.3751.82735325641.375100
2.31-2.4510.70.0140.82612724510.919100
2.45-2.6210.60.0141.32444722990.566100
2.62-2.8310.50.0141.72266221490.32100
2.83-3.110.50.0143.92092219930.181100
3.1-3.4610.40.0145.81886618190.111100
3.46-410.20.0147.21645116170.085100
4-4.99.90.014101369413900.059100
4.9-6.939.30.01413.21032111060.044100
6.93-1069.20.01416.462416760.03299.9

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.19→77.152 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.416 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.179
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. RESIDUES 1, 25-37, 119-125 IN CHAIN A AND 1, 25-37 IN CHAIN B ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 917 5.1 %RANDOM
Rwork0.201 ---
obs0.203 18015 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.913 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.19→77.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 0 57 1811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211839
X-RAY DIFFRACTIONr_bond_other_d0.0050.021247
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.9412499
X-RAY DIFFRACTIONr_angle_other_deg1.61433046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2235223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12723.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.4715335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6151512
X-RAY DIFFRACTIONr_chiral_restr0.1160.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022010
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02368
X-RAY DIFFRACTIONr_nbd_refined0.150.2271
X-RAY DIFFRACTIONr_nbd_other0.1310.21181
X-RAY DIFFRACTIONr_nbtor_refined0.1370.2829
X-RAY DIFFRACTIONr_nbtor_other0.0660.2894
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1340.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0770.26
X-RAY DIFFRACTIONr_mcbond_it1.9431333
X-RAY DIFFRACTIONr_mcbond_other0.3563442
X-RAY DIFFRACTIONr_mcangle_it2.6451764
X-RAY DIFFRACTIONr_scbond_it4.3518872
X-RAY DIFFRACTIONr_scangle_it5.8511729
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1392 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.465
LOOSE THERMAL3.5110
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 67 -
Rwork0.29 1220 -
obs-1287 99.69 %
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)
14.7275-1.89260.18482.27450.72532.04660.10840.2982-0.1561-0.1274-0.0590.25410.03550.1094-0.0494-0.2870.0347-0.0374-0.2925-0.0292-0.037448.58760.966-33.747
26.0764-0.3506-1.05363.6942-0.37193.40370.02370.6839-0.5105-0.20630.1639-0.05830.29320.3132-0.1876-0.210.0849-0.0136-0.0955-0.1175-0.010765.41552.784-37.934
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 243 - 25
21AA38 - 11839 - 119
32BB2 - 243 - 25
42BB38 - 12439 - 125

+
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