[English] 日本語
Yorodumi
- PDB-3kzt: Crystal structure of Protein of unknown function (NP_812423.1) fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kzt
TitleCrystal structure of Protein of unknown function (NP_812423.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / Protein of unknown function / 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, / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta / DUF3828 domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Protein of unknown function (NP_812423.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / 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: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6999
Polymers32,1962
Non-polymers5027
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-28 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.698, 46.261, 130.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5 / Auth seq-ID: 36 - 165 / Label seq-ID: 12 - 141

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

-
Components

#1: Protein uncharacterized protein


Mass: 16098.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_3511 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A1Z7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE THIS CONSTRUCT (RESIDUES 26-167) WAS EXPRESSED WITH THE PURIFICATION TAG ...SEQUENCE THIS CONSTRUCT (RESIDUES 26-167) WAS EXPRESSED WITH THE 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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 3.0000M ammonium sulfate, 0.1M MES pH 5.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97916
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2009 / 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
20.979161
ReflectionResolution: 2.1→28.56 Å / Num. obs: 16114 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.795 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.153.50.6291.2390611310.629100
2.15-2.213.50.521.5400111570.52100
2.21-2.283.50.4931.6385011130.493100
2.28-2.353.40.411.8370510760.41100
2.35-2.423.50.3782363410510.37899.9
2.42-2.513.50.322.434539980.32100
2.51-2.63.40.272.834189910.27100
2.6-2.713.50.2373.232409390.237100
2.71-2.833.40.1864.130939040.186100
2.83-2.973.40.1474.830018770.147100
2.97-3.133.40.1295.528448380.129100
3.13-3.323.40.1026.926967970.102100
3.32-3.553.40.0828.225467520.08299.9
3.55-3.833.40.078.623196890.0799.8
3.83-4.23.30.05910.321726510.05999.9
4.2-4.73.30.05111.819365820.05199.8
4.7-5.423.20.05510.717065310.05599.8
5.42-6.643.20.0619.814474580.06199.7
6.64-9.393.10.04711.311253630.04799.8
9.39-28.562.80.037135972160.03795.6

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→28.56 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 14.661 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.224
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ETHYLENE GLYCOL (EDO) AND SULFATE IONS (SO4) FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 5. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 805 5 %RANDOM
Rwork0.222 ---
obs0.224 16067 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68 Å2 / Biso mean: 18.402 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2--1.62 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 30 118 2192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222264
X-RAY DIFFRACTIONr_bond_other_d0.0040.021522
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9693089
X-RAY DIFFRACTIONr_angle_other_deg1.18833757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1275306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42225.798119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49115417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6351514
X-RAY DIFFRACTIONr_chiral_restr0.10.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022573
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02427
X-RAY DIFFRACTIONr_mcbond_it0.2821.51379
X-RAY DIFFRACTIONr_mcbond_other0.0571.5554
X-RAY DIFFRACTIONr_mcangle_it0.52622251
X-RAY DIFFRACTIONr_scbond_it0.8563885
X-RAY DIFFRACTIONr_scangle_it1.3444.5816
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
744MEDIUM POSITIONAL0.240.5
851LOOSE POSITIONAL0.475
744MEDIUM THERMAL0.32
851LOOSE THERMAL0.2910
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 66 -
Rwork0.298 1059 -
all-1125 -
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)
16.16990.9824.48530.98960.42545.5955-0.07980.17610.069-0.02280.0768-0.1154-0.10140.23570.0030.2593-0.02790.01620.2108-0.02290.051330.83615.19912.893
211.3219-1.87552.07922.7397-1.16061.7702-0.49190.26251.4672-0.23330.1395-0.4355-0.5440.1950.35240.3756-0.0887-0.06780.2019-0.03440.231536.28927.21819.819
31.82410.2394.34319.02890.249510.50430.0227-0.0581-0.1059-0.08280.1458-0.2164-0.02060.11-0.16860.2625-0.07190.00590.47840.07860.071236.82615.40427.616
43.4734-1.83293.94342.0385-3.07466.0771-0.0907-0.257-0.10670.02570.16340.1104-0.143-0.2722-0.07270.26570.01770.02310.2181-0.0270.034126.89116.34421.055
50.53910.2986-0.22516.5258-3.0162.5106-0.01560.0082-0.07080.04840.23850.10260.058-0.3442-0.22290.3041-0.02540.00090.17250.00520.07145.541-9.43224.044
61.24861.2875-1.26734.53751.39723.690.4319-0.18050.20530.2349-0.1615-0.0524-0.44840.1671-0.27040.3542-0.05620.13360.2634-0.04610.196350.96810.80414.923
71.8162-0.18450.84694.2229-1.93683.9242-0.04980.0576-0.1325-0.2299-0.232-0.51840.2940.66990.28190.30630.03160.07670.30110.0310.110557.9492.6226.773
81.4565-1.32931.95472.1542-2.86455.3480.10810.0141-0.0391-0.14130.00120.10990.31210.1187-0.10940.2524-0.00530.02060.19590.00420.025846.393-4.00311.528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 74
2X-RAY DIFFRACTION2A75 - 100
3X-RAY DIFFRACTION3A101 - 116
4X-RAY DIFFRACTION4A117 - 166
5X-RAY DIFFRACTION5B36 - 62
6X-RAY DIFFRACTION6B63 - 87
7X-RAY DIFFRACTION7B88 - 109
8X-RAY DIFFRACTION8B110 - 165

+
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