[English] 日本語
Yorodumi
- PDB-3blz: Crystal structure of a ntf2-like protein of unknown function (sba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3blz
TitleCrystal structure of a ntf2-like protein of unknown function (sbal_0622) from shewanella baltica os155 at 1.75 A resolution
ComponentsNTF2-like protein of unknown function
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyPutative lumazine-binding / Putative lumazine-binding / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesShewanella baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a NTF2-like protein of unknown function (YP_001049020.1) from Shewanella baltica OS155 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / 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 1.4Jan 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
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 (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NTF2-like protein of unknown function
B: NTF2-like protein of unknown function
C: NTF2-like protein of unknown function
D: NTF2-like protein of unknown function
E: NTF2-like protein of unknown function
F: NTF2-like protein of unknown function
G: NTF2-like protein of unknown function
H: NTF2-like protein of unknown function
I: NTF2-like protein of unknown function
J: NTF2-like protein of unknown function
K: NTF2-like protein of unknown function
L: NTF2-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,70042
Polymers168,75012
Non-polymers1,95030
Water20,8611158
1
A: NTF2-like protein of unknown function
B: NTF2-like protein of unknown function
C: NTF2-like protein of unknown function
D: NTF2-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,85313
Polymers56,2504
Non-polymers6039
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
MethodPISA
2
E: NTF2-like protein of unknown function
F: NTF2-like protein of unknown function
G: NTF2-like protein of unknown function
H: NTF2-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,03916
Polymers56,2504
Non-polymers78912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
MethodPISA
3
I: NTF2-like protein of unknown function
J: NTF2-like protein of unknown function
K: NTF2-like protein of unknown function
L: NTF2-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,80813
Polymers56,2504
Non-polymers5599
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.085, 58.121, 140.462
Angle α, β, γ (deg.)80.930, 78.430, 60.600
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASN / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 3 - 125 / Label seq-ID: 4 - 126

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL

-
Components

#1: Protein
NTF2-like protein of unknown function


Mass: 14062.471 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella baltica (bacteria) / Strain: OS155 / Gene: YP_001049020.1, Sbal_0622 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3D088
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1158 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: NANODROP, 20.0% 2-propanol, 20.0% PEG 4000, 0.1M Citric acid pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0000, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
ReflectionResolution: 1.75→29.348 Å / Num. obs: 126809 / % possible obs: 81.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.81.90.4561.5805443450.45637.8
1.8-1.841.90.3561.9985152540.35646.6
1.84-1.91.90.2892.31171762390.28957.6
1.9-1.961.80.2133.31403976610.21372.5
1.96-2.021.80.1654.31740694340.16592
2.02-2.091.90.1451788491900.1492.8
2.09-2.171.90.1086.61731988930.10892.7
2.17-2.261.90.0868.21661085450.08693.1
2.26-2.361.90.0779.21594381920.07793
2.36-2.471.90.06410.81535278820.06493.2
2.47-2.611.90.05811.51451474640.05893.1
2.61-2.771.90.0479.81380870860.04793.1
2.77-2.961.90.03816.21278765940.03893.4
2.96-3.21.90.03319.41200262170.03393.1
3.2-3.51.90.02820.81087256650.02893.1
3.5-3.911.90.02620.6981851280.02692.8
3.91-4.521.90.02423.3841644960.02492.5
4.52-5.531.70.02421.2666138150.02493
5.53-7.831.90.02324.2591930500.02396.5
7.83-29.34820.01926329616590.01994.8

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.75→29.348 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.559 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.123
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. PEG 4000 FRAGMENTS (PEG) FROM CRYSTALLIZATION CONDITIONS AND ETHYLENE GLYCOL (EDO) FROM CRYO CONDITIONS ARE MODELED IN THE STRUCTURE. 5. THE NOMINAL RESOLUTION IS 1.90 A WITH 16060 OBSERVED REFLECTIONS BETWEEN 1.90-1.75 (47.4% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 6400 5 %RANDOM
Rwork0.152 ---
obs0.154 126808 81.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0.23 Å2-0.31 Å2
2--0.22 Å21.05 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11418 0 126 1158 12702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02212337
X-RAY DIFFRACTIONr_bond_other_d0.0010.028137
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.93216799
X-RAY DIFFRACTIONr_angle_other_deg0.934319863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46351585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22723.829538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.602151905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9741555
X-RAY DIFFRACTIONr_chiral_restr0.0920.21884
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214069
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022622
X-RAY DIFFRACTIONr_nbd_refined0.2070.22242
X-RAY DIFFRACTIONr_nbd_other0.20.28255
X-RAY DIFFRACTIONr_nbtor_refined0.1770.26037
X-RAY DIFFRACTIONr_nbtor_other0.0860.26214
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2965
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.221
X-RAY DIFFRACTIONr_mcbond_it1.94638454
X-RAY DIFFRACTIONr_mcbond_other0.66733116
X-RAY DIFFRACTIONr_mcangle_it2.55512566
X-RAY DIFFRACTIONr_scbond_it4.30485106
X-RAY DIFFRACTIONr_scangle_it5.753114233
Refine LS restraints NCS

Ens-ID: 1 / Number: 1377 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.180.5
2BMEDIUM POSITIONAL0.180.5
3CMEDIUM POSITIONAL0.180.5
4DMEDIUM POSITIONAL0.230.5
5EMEDIUM POSITIONAL0.230.5
6FMEDIUM POSITIONAL0.190.5
7GMEDIUM POSITIONAL0.340.5
8HMEDIUM POSITIONAL0.220.5
9IMEDIUM POSITIONAL0.230.5
10JMEDIUM POSITIONAL0.220.5
11KMEDIUM POSITIONAL0.180.5
12LMEDIUM POSITIONAL0.220.5
1AMEDIUM THERMAL0.92
2BMEDIUM THERMAL0.922
3CMEDIUM THERMAL1.012
4DMEDIUM THERMAL0.92
5EMEDIUM THERMAL0.922
6FMEDIUM THERMAL0.832
7GMEDIUM THERMAL0.892
8HMEDIUM THERMAL0.912
9IMEDIUM THERMAL0.952
10JMEDIUM THERMAL0.892
11KMEDIUM THERMAL0.882
12LMEDIUM THERMAL0.852
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 215 -
Rwork0.242 4013 -
all-4228 -
obs--36.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.82160.5642-0.38791.3146-0.19321.2024-0.04030.13960.0659-0.15550.09050.0022-0.13250.0779-0.0502-0.0337-0.06360.0231-0.0705-0.0024-0.056952.96916.732771.455
21.03540.3041-0.02641.6708-0.11941.17860.14-0.08840.10870.3147-0.07380.1467-0.2012-0.0152-0.06620.0235-0.06770.0577-0.1063-0.0294-0.039546.77998.773591.5981
30.80730.364-0.06921.5128-0.4331.0740.0357-0.06130.00640.1545-0.0040.04640.1407-0.0819-0.0317-0.0164-0.0623-0.013-0.09730.0072-0.071138.6413-17.762489.2009
40.5460.3006-0.00991.1807-0.16371.4927-0.05520.17750.0688-0.19830.140.18660.1393-0.2741-0.0848-0.0296-0.0965-0.0514-0.02490.0389-0.024232.3331-12.034969.6743
51.6277-0.0358-0.28510.6094-0.01841.6970.08640.2338-0.0594-0.1071-0.049-0.0650.12040.1577-0.0374-0.09840.0380.00210.0483-0.0264-0.063368.00134.269224.0535
61.8010.08610.00270.4473-0.24511.12520.0941-0.24930.08150.0383-0.0670.0126-0.04890.1636-0.0271-0.1185-0.02060.00310.0467-0.0234-0.063268.48469.385544.801
71.71410.0864-0.44080.4577-0.27521.24740.0777-0.1518-0.05360.02890.0053-0.00150.0419-0.1368-0.083-0.1173-0.0155-0.0110.02590.0398-0.054441.25853.381544.2302
81.7738-0.21870.08250.6568-0.46951.39770.11630.27320.1122-0.05750.00320.0908-0.0779-0.1877-0.1196-0.10120.03550.00760.06250.0594-0.042941.394812.764925.0826
91.2499-0.77950.19021.7937-0.1192.16370.20.1116-0.2427-0.4197-0.09350.29320.457-0.008-0.10650.14150.0614-0.0942-0.1111-0.03260.000745.53476.86-22.5086
101.0467-0.93510.4121.902-0.53411.4083-0.1005-0.1546-0.10540.13910.14840.10530.19610.1026-0.04790.01360.089-0.0079-0.06860.002-0.061352.32778.4412-2.3523
110.8184-0.6610.0411.7316-0.06571.5836-0.1356-0.1903-0.10930.25140.21650.2384-0.1421-0.2749-0.08090.00580.09720.0542-0.03120.0477-0.020133.563329.0444-0.4331
120.8037-0.6748-0.02231.7864-0.6331.42240.08050.07820.0297-0.2320.00560.0326-0.1664-0.0643-0.0860.02790.04340.0185-0.09160.0109-0.04939.710734.0733-20.0374
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1264 - 127
2X-RAY DIFFRACTION2BB3 - 1264 - 127
3X-RAY DIFFRACTION3CC3 - 1264 - 127
4X-RAY DIFFRACTION4DD3 - 1264 - 127
5X-RAY DIFFRACTION5EE3 - 1264 - 127
6X-RAY DIFFRACTION6FF3 - 1254 - 126
7X-RAY DIFFRACTION7GG3 - 1264 - 127
8X-RAY DIFFRACTION8HH3 - 1254 - 126
9X-RAY DIFFRACTION9II3 - 1254 - 126
10X-RAY DIFFRACTION10JJ3 - 1264 - 127
11X-RAY DIFFRACTION11KK3 - 1254 - 126
12X-RAY DIFFRACTION12LL3 - 1254 - 126

+
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