[English] 日本語
Yorodumi
- PDB-2q22: Crystal structure of uncharacterized protein (YP_323524.1) from A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q22
TitleCrystal structure of uncharacterized protein (YP_323524.1) from Anabaena variabilis ATCC 29413 at 2.11 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / YP_323524.1 / uncharacterized protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyProtein of unknown function DUF1824 / Domain of unknown function (DUF1824) / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / 2-Layer Sandwich / Alpha Beta / ACETATE ION / Uncharacterized protein
Function and homology information
Biological speciesAnabaena variabilis ATCC 29413 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.11 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (YP_323524.1) from Anabaena variabilis ATCC 29413 at 2.11 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 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 1.6Jan 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 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK ... THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A OLIGOMERIZATION STATE IN SOLUTION.
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,32014
Polymers46,4653
Non-polymers85511
Water3,441191
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8365
Polymers15,4881
Non-polymers3484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8125
Polymers15,4881
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6714
Polymers15,4881
Non-polymers1833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.374, 103.374, 42.086
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: LEU / End label comp-ID: VAL / Refine code: 2 / Auth seq-ID: 9 - 138 / Label seq-ID: 10 - 139

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A OLIGOMERIZATION STATE IN SOLUTION.

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Uncharacterized protein


Mass: 15488.285 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria)
Species: Anabaena variabilis / Strain: PCC 7937 / Gene: YP_323524.1, Ava_3019 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3M8Q7

-
Non-polymers , 5 types, 202 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.18
Details: NANODROP, 5.0% PEG 1000, 48.3% Ethylene glycol, 0.1M Sodium acetate pH 4.18, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97939
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 1, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979391
ReflectionResolution: 2.11→29.841 Å / Num. obs: 28912 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 29.62 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.11-2.163.80.6511.2788020800.651100
2.16-2.223.80.5631.3797821260.563100
2.22-2.293.80.5131.4753119940.513100
2.29-2.363.80.4341.7756120080.434100
2.36-2.443.80.3722725719110.372100
2.44-2.523.80.3242.3695518370.324100
2.52-2.623.80.2842.6680017880.284100
2.62-2.723.80.2393.1648717220.239100
2.72-2.853.80.1883.8624216440.188100
2.85-2.983.80.1564.6592815600.156100
2.98-3.153.80.1255.5571215120.125100
3.15-3.343.80.1086.3533914120.108100
3.34-3.573.80.0887.3499513270.088100
3.57-3.853.80.0767.3475412580.076100
3.85-4.223.80.0649.8425911240.064100
4.22-4.723.80.05910.6396410420.059100
4.72-5.453.80.05710.434248960.057100
5.45-6.673.80.0649.929167640.064100
6.67-9.443.80.0511.922675930.0599.9
9.44-29.843.70.05111.411583140.05196.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.11→29.841 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.689 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.163
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. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. PG4, ACT, CL AND EDO ARE MODELED BASED ON CRYSTALLIZATION/CRYO CONDITIONS. 5. THE DATA APPEAR TWINNED. IT COULD BE DUE TO THE PRESENCE OF PSEUDO-TRANSLATION. REFINEMENT CONSIDERING TWINNING DOES NOT IMPROVE MAPS OR REFINEMENT STATISTICS. AS A RESULT, THE POSSIBLE TWINNING IS NOT CONSIDERED IN THE FINAL REFINEMENT. 6. RESIDUES A/B1-7, C1-8 AND A/B/C81 ARE DISORDERED AND NOT INCLUDED IN THE FINAL MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1467 5.1 %RANDOM
Rwork0.191 ---
obs0.193 28891 100 %-
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: 33.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0.37 Å20 Å2
2---0.75 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.11→29.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2966 0 53 191 3210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223084
X-RAY DIFFRACTIONr_bond_other_d0.0020.022045
X-RAY DIFFRACTIONr_angle_refined_deg1.5212.0084171
X-RAY DIFFRACTIONr_angle_other_deg0.93335049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4665391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52624.685111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51815517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.002157
X-RAY DIFFRACTIONr_chiral_restr0.0920.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023363
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02560
X-RAY DIFFRACTIONr_nbd_refined0.2110.2629
X-RAY DIFFRACTIONr_nbd_other0.1880.21999
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21422
X-RAY DIFFRACTIONr_nbtor_other0.0880.21691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2141
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.220
X-RAY DIFFRACTIONr_mcbond_it2.1832100
X-RAY DIFFRACTIONr_mcbond_other0.3643795
X-RAY DIFFRACTIONr_mcangle_it3.2453127
X-RAY DIFFRACTIONr_scbond_it5.36381244
X-RAY DIFFRACTIONr_scangle_it6.998111041
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A752TIGHT POSITIONAL0.040.05
2B752TIGHT POSITIONAL0.050.05
3C752TIGHT POSITIONAL0.040.05
1A864MEDIUM POSITIONAL0.170.5
2B864MEDIUM POSITIONAL0.210.5
3C864MEDIUM POSITIONAL0.220.5
1A752TIGHT THERMAL0.190.5
2B752TIGHT THERMAL0.180.5
3C752TIGHT THERMAL0.190.5
1A864MEDIUM THERMAL0.92
2B864MEDIUM THERMAL0.952
3C864MEDIUM THERMAL0.952
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 110 -
Rwork0.223 1958 -
obs-2068 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)
11.6003-0.1997-0.11112.45040.22380.5701-0.0058-0.0577-0.27510.03360.0108-0.1020.0588-0.0496-0.005-0.0579-0.01010.0011-0.08150.0027-0.0741-2.419141.6515.6962
22.87451.26260.6141.5760.05570.98160.09150.04110.0413-0.0373-0.0767-0.1895-0.1470.093-0.0148-0.0148-0.02880.0234-0.0226-0.002-0.0208-36.949440.97467.3491
31.97670.55430.03542.9438-0.1021.44290.0434-0.0270.07110.0595-0.0757-0.53190.04880.20770.0323-0.02440.0270.00120.01770.01150.034514.239811.1757.2833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 1389 - 139
2X-RAY DIFFRACTION2BB8 - 1389 - 139
3X-RAY DIFFRACTION3CC9 - 13810 - 139

+
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