[English] 日本語
Yorodumi
- PDB-2r4i: CRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN (CHU_1428) FROM CYTOPHAG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r4i
TitleCRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN (CHU_1428) FROM CYTOPHAGA HUTCHINSONII ATCC 33406 AT 1.60 A RESOLUTION
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / NTF2-LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyNuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / CITRIC ACID / ISOPROPYL ALCOHOL / Uncharacterized protein
Function and homology information
Biological speciesCytophaga hutchinsonii ATCC 33406 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF2-like protein of unknown function (YP_678039.1) from Cytophaga hutchinsonii ATCC 33406 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,52815
Polymers55,6714
Non-polymers85711
Water7,746430
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,57211
Polymers27,8352
Non-polymers7379
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9554
Polymers27,8352
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.830, 57.690, 157.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein
Uncharacterized protein


Mass: 13917.635 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii ATCC 33406 (bacteria)
Species: Cytophaga hutchinsonii / Strain: NCIMB 9469 / Gene: YP_678039.1, CHU_1428 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q11V67
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: NANODROP, 5.0% Glycerol, 19.0% Isopropanol, 19.0% PEG 4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97926, 0.97904
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 25, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979261
30.979041
ReflectionResolution: 1.6→28.843 Å / Num. obs: 67050 / % possible obs: 89.2 % / Biso Wilson estimate: 26.306 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 14.02
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allDiffraction-ID% possible all
1.6-1.660.3462.31855311455182.3
1.66-1.720.2882.71677710208185.5
1.72-1.80.2153.71979611993188.4
1.8-1.90.1455.22079512473189.9
1.9-2.020.0977.91989811961190.3
2.02-2.170.06611.41962011646191.7
2.17-2.390.05152104312230191.6
2.39-2.730.03620.12100111964191.8
2.73-28.8430.02329.32198912165191.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→28.843 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.291 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.086
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. ONE CITRATE ANION, EIGHT ISOPROPYL ALCOHOL, AND TWO GLYCEROL MOLECULE(S) HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 3377 5 %RANDOM
Rwork0.175 ---
all0.176 ---
obs0.176 66987 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.686 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2---0.4 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 57 430 4239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224022
X-RAY DIFFRACTIONr_bond_other_d0.0050.022585
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.9635500
X-RAY DIFFRACTIONr_angle_other_deg1.3673.0016370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7075522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93325.028177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.60815706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1181519
X-RAY DIFFRACTIONr_chiral_restr0.0990.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024438
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02765
X-RAY DIFFRACTIONr_nbd_refined0.1910.3645
X-RAY DIFFRACTIONr_nbd_other0.1660.32672
X-RAY DIFFRACTIONr_nbtor_refined0.1610.51895
X-RAY DIFFRACTIONr_nbtor_other0.0850.52001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.5595
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0330.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.365
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.547
X-RAY DIFFRACTIONr_mcbond_it1.90732589
X-RAY DIFFRACTIONr_mcbond_other0.51131005
X-RAY DIFFRACTIONr_mcangle_it2.75454063
X-RAY DIFFRACTIONr_scbond_it4.59381676
X-RAY DIFFRACTIONr_scangle_it6.029111413
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 275 -
Rwork0.234 4603 -
obs-4878 96.27 %
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)
10.72870.2189-0.30091.0986-0.39750.97240.01970.08920.0404-0.11350.03830.0820.0413-0.188-0.058-0.01380.00520.0006-0.09280.014-0.056152.813916.751831.3075
20.7318-0.3191-0.19241.67880.29721.15010.0085-0.09540.00010.0553-0.0112-0.3570.03760.24040.0027-0.03290.00820.0001-0.0510.01050.038274.649413.691134.6854
30.96630.13420.24781.6591-0.66571.7972-0.09430.2822-0.1819-0.27230.0762-0.14510.35480.06270.01810.0158-0.00630.02640.0441-0.0003-0.025664.484624.94881.0799
41.01230.26740.08340.64870.1121.1406-0.0128-0.0210.1320.07540.03730.0327-0.091-0.0408-0.0245-0.06640.0140.00390.01510.0494-0.041161.166644.29319.9443
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 1221 - 123
22BB1 - 1212 - 122
33CC2 - 1213 - 122
44DD6 - 1227 - 123

+
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