[English] 日本語
Yorodumi
- PDB-3ecf: Crystal structure of an ntf2-like protein (ava_4193) from anabaen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ecf
TitleCrystal structure of an ntf2-like protein (ava_4193) from anabaena variabilis atcc 29413 at 1.90 A resolution
ComponentsNTF2-like Protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyDomain of unknown function DUF4904 / Domain of unknown function (DUF4904) / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Unknown ligand / DUF4904 domain-containing protein
Function and homology information
Biological speciesAnabaena variabilis ATCC 29413 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NTF2-like Protein (YP_324687.1) from ANABAENA VARIABILIS ATCC 29413 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: 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 1.4Feb 1, 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 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NTF2-like Protein
B: NTF2-like Protein
C: NTF2-like Protein
D: NTF2-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,01411
Polymers60,7264
Non-polymers2887
Water6,900383
1
A: NTF2-like Protein
B: NTF2-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5556
Polymers30,3632
Non-polymers1924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-34 kcal/mol
Surface area11010 Å2
MethodPISA
2
C: NTF2-like Protein
hetero molecules

C: NTF2-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5556
Polymers30,3632
Non-polymers1924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3840 Å2
ΔGint-59 kcal/mol
Surface area11060 Å2
MethodPISA
3
D: NTF2-like Protein

D: NTF2-like Protein


Theoretical massNumber of molelcules
Total (without water)30,3634
Polymers30,3632
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3090 Å2
ΔGint-20 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.056, 74.056, 189.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein
NTF2-like Protein


Mass: 15181.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria)
Gene: YP_324687.1, Ava_4193 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3M5E4
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.4000M (NH4)2SO4, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97864
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 6, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978641
ReflectionResolution: 1.9→29.323 Å / Num. obs: 42557 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 15.218 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.154 / Net I/σ(I): 4.213
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.957.30.6681.12242230890.668100
1.95-27.30.5571.42182729970.557100
2-2.067.30.4671.62141529360.467100
2.06-2.127.30.4241.82061328330.424100
2.12-2.197.30.3652.12001127490.365100
2.19-2.277.30.3132.41952626870.313100
2.27-2.367.30.2842.71869225720.284100
2.36-2.457.30.25531822825100.255100
2.45-2.567.20.2423.11741624050.242100
2.56-2.697.30.2083.61659922880.208100
2.69-2.837.20.1841600822130.18100
2.83-37.20.154.71504520890.15100
3-3.217.20.1185.51408319570.118100
3.21-3.477.20.0966.51310018310.096100
3.47-3.87.10.07181220517120.071100
3.8-4.257.10.0658.51107615670.065100
4.25-4.9170.0579966813880.057100
4.91-6.016.80.0697.7820112010.069100
6.01-8.56.60.0736.962669550.073100
8.5-29.335.80.0537.633775780.05397.6

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.323 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.361 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.145
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. SO4 MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 5. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED IN THE PUTATIVE ACTIVE SITE OF EACH MONOMER. THE UNL BEARS STRONG SIMILARITY TO BENZOATE IN SHAPE.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2144 5 %RANDOM
Rwork0.182 ---
obs0.184 42468 99.95 %-
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 max: 73.8 Å2 / Biso mean: 21.847 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4125 0 51 383 4559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224355
X-RAY DIFFRACTIONr_bond_other_d0.0040.022882
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9615939
X-RAY DIFFRACTIONr_angle_other_deg1.32337037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6955530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23324.227194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.67515715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9991516
X-RAY DIFFRACTIONr_chiral_restr0.10.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024815
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02913
X-RAY DIFFRACTIONr_nbd_refined0.1740.2729
X-RAY DIFFRACTIONr_nbd_other0.1480.22794
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22058
X-RAY DIFFRACTIONr_nbtor_other0.0730.22176
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2345
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2080.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.239
X-RAY DIFFRACTIONr_mcbond_it1.43722969
X-RAY DIFFRACTIONr_mcbond_other0.26121041
X-RAY DIFFRACTIONr_mcangle_it2.01144239
X-RAY DIFFRACTIONr_scbond_it3.87261987
X-RAY DIFFRACTIONr_scangle_it5.02881691
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 142 -
Rwork0.188 2943 -
all-3085 -
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)
11.485-0.114-0.32850.70220.1330.58830.0513-0.14110.01080.1284-0.015-0.0352-0.00320.0574-0.0363-0.0291-0.0044-0.0132-0.0237-0.0006-0.065712.92330.52654.995
20.5282-0.06710.36331.8661-0.22510.936-0.00330.1408-0.0161-0.16030.0268-0.02530.03870.0391-0.0235-0.0326-0.00120.0062-0.0223-0.0054-0.07535.31923.4935.442
31.91310.0189-0.16890.87480.20280.54280.04-0.2175-0.01660.0932-0.0534-0.0490.0160.01590.0134-0.04410.005-0.0195-0.01590.0025-0.067813.462-5.85757.029
41.503-0.02870.03040.86330.31610.76920.01780.21050.0061-0.108-0.0262-0.0741-0.00450.02180.0085-0.0422-0.00440.0168-0.01280.007-0.067812.8555.74384.802
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1293 - 130
2X-RAY DIFFRACTION2BB2 - 1293 - 130
3X-RAY DIFFRACTION3CC2 - 1293 - 130
4X-RAY DIFFRACTION4DD2 - 1293 - 130

+
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