[English] 日本語
Yorodumi
- PDB-3kdq: Crystal structure of a functionally unknown conserved protein fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kdq
TitleCrystal structure of a functionally unknown conserved protein from Corynebacterium diphtheriae.
Componentsuncharacterized conserved protein
Keywordsstructural genomics / unknown function / functionally unknown protein / Corynebacterium diphtheriae / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyFerritin / Ferritin - #10 / : / Family of unknown function (DUF6847) / Helix non-globular / Special / Septicolysin
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsZhang, R. / Wu, R. / Tan, K. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a functionally unknown conserved protein from Corynebacterium diphtheriae.
Authors: Zhang, R. / Wu, R. / Tan, K. / Clancy, S. / Joachimiak, A.
History
DepositionOct 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: uncharacterized conserved protein
B: uncharacterized conserved protein
C: uncharacterized conserved protein
D: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)72,1474
Polymers72,1474
Non-polymers00
Water00
1
A: uncharacterized conserved protein
B: uncharacterized conserved protein
C: uncharacterized conserved protein
D: uncharacterized conserved protein

A: uncharacterized conserved protein
B: uncharacterized conserved protein
C: uncharacterized conserved protein
D: uncharacterized conserved protein

A: uncharacterized conserved protein
B: uncharacterized conserved protein
C: uncharacterized conserved protein
D: uncharacterized conserved protein

A: uncharacterized conserved protein
B: uncharacterized conserved protein
C: uncharacterized conserved protein
D: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)288,58816
Polymers288,58816
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area71020 Å2
ΔGint-151 kcal/mol
Surface area113950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.676, 132.484, 176.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 0:28 or resseq 39:52 or resseq...
211chain B and (resseq 0:28 or resseq 39:52 or resseq...
311chain C and (resseq 0:28 or resseq 39:52 or resseq...
411chain D and (resseq 0:28 or resseq 39:52 or resseq...
DetailsExperimentally unknown. It is predicted that the four chains (A,B,C and D)and their symmetry-related molecules generated by operators (1-x,y,-z), (1-x,-y,z) and (1+x,-y,-z) respectively, form an assemble of sixteen molecules.

-
Components

#1: Protein
uncharacterized conserved protein


Mass: 18036.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: Corynebacterium diphtheriae, DIP1984 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6NFB0
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Na-Hepes, 200mM Na Nitrate, 30% PEG400 , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97940, 0.97953
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2009 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.979531
ReflectionResolution: 3→48.5 Å / Num. all: 18599 / Num. obs: 18599 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 29
Reflection shellResolution: 3→3.05 Å / Redundancy: 7 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 3.1 / Num. unique all: 895 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3→48.461 Å / SU ML: 0.39 / σ(F): 1.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 1796 5.12 %random
Rwork0.1971 ---
all0.2006 35075 --
obs0.2006 35075 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.758 Å2 / ksol: 0.327 e/Å3
Refinement stepCycle: LAST / Resolution: 3→48.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4939 0 0 0 4939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014979
X-RAY DIFFRACTIONf_angle_d1.2716719
X-RAY DIFFRACTIONf_dihedral_angle_d21.1981931
X-RAY DIFFRACTIONf_chiral_restr0.081781
X-RAY DIFFRACTIONf_plane_restr0.003887
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A907X-RAY DIFFRACTIONPOSITIONAL
12B907X-RAY DIFFRACTIONPOSITIONAL0.04
13C896X-RAY DIFFRACTIONPOSITIONAL0.04
14D907X-RAY DIFFRACTIONPOSITIONAL0.043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9997-3.10690.36821790.29963284X-RAY DIFFRACTION99
3.1069-3.23130.37291950.29913318X-RAY DIFFRACTION100
3.2313-3.37830.40461810.27513328X-RAY DIFFRACTION100
3.3783-3.55640.33711750.24833361X-RAY DIFFRACTION100
3.5564-3.77910.29412040.21893308X-RAY DIFFRACTION100
3.7791-4.07080.25171600.17993329X-RAY DIFFRACTION100
4.0708-4.48020.25231810.16763358X-RAY DIFFRACTION100
4.4802-5.12790.19271960.14453313X-RAY DIFFRACTION100
5.1279-6.45820.27181780.18963334X-RAY DIFFRACTION100
6.4582-48.46770.19011470.16213346X-RAY DIFFRACTION99
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.3606-0.98890.27071.4539-1.08870.76780.00571.28270.52730.2787-0.8140.0174-0.08660.45810.62950.3169-0.1013-0.08470.6983-0.28410.770166.052431.09138.2054
25.1426-3.05862.12876.1634-0.43091.08951.44610.79470.107-0.6944-1.2915-0.1217-0.1642-0.51560.15650.32480.39230.08760.7165-0.10990.4605
31.74920.65250.86132.64610.56130.262-0.2786-0.07130.56830.53630.1237-0.56350.0060.07670.07770.5016-0.2517-0.0770.474-0.10090.797
48.2383-4.30556.15234.3699-4.16375.0885-0.7869-0.8232-0.9558-0.76230.4711-1.52230.1208-0.50020.30350.58620.1817-0.10560.5041-0.13621.3751
51.25620.5217-0.12070.2375-0.26921.1976-0.13090.09450.0115-0.27320.4857-0.221-0.2159-0.0051-0.33540.6210.01990.01360.2206-0.18560.8845
62.12641.2021.30385.07993.9753.7074-0.90940.16270.61130.44121.51380.38050.09670.5108-0.12640.2905-0.2699-0.02560.19590.08730.6578
72.6452-1.65280.27531.9851-0.14220.67540.2040.62260.28670.63390.1894-0.4290.24330.1291-0.28780.53030.0649-0.06930.2949-0.03250.7105
81.4191-0.87761.96430.8399-0.8092.84670.0464-0.2249-0.86860.00670.46190.56250.1254-0.1323-0.46710.22140.08550.05530.6308-0.29840.6499
96.2878-1.38975.73421.04070.06828.54652.4174-1.0299-2.2542-0.40330.3691-0.6624-0.2254-0.0785-2.12770.0857-0.0828-0.54870.54010.1440.6998
103.5284-0.0341-0.87510.06820.14570.44230.2473-1.0470.18620.0499-0.08890.0263-0.1611-0.5711-0.02420.48070.21880.18460.8625-0.14030.4101
113.99060.9943-5.04574.5008-4.43558.7425-1.2886-1.90751.3824-1.54910.2596-1.0223-0.36010.97150.59580.3016-0.0976-0.09111.5454-0.42840.2533
123.2102-0.5671-1.57761.7851.23371.06180.12420.723-0.3168-0.2014-0.55010.2017-0.2413-0.70480.31660.30780.0742-0.03060.7638-0.16990.1838
131.6899-0.9758-1.71380.56740.90481.5975-0.331-0.7721-0.04930.5150.1-0.17240.49010.9420.1710.20120.13360.27270.7630.04330.2993
142.8094-0.43422.36761.2116-0.37292.00960.2075-0.9158-0.35010.038-0.29850.1148-0.3286-0.18090.09880.42030.0726-0.08130.7782-0.05080.2949
154.94333.4145.54444.0054.94048.00670.3686-0.5192-1.440.23010.713-0.91630.118-0.6711-0.89120.27420.1170.01990.33960.00150.6618
163.00240.2027-0.14548.00078.73199.31271.7819-0.6744-1.98910.2882-2.2767-0.8711-0.1891-1.92450.63740.2045-0.4685-0.02450.6244-0.1820.7151
175.99661.42251.86362.67792.36092.3724-0.0791-0.32181.7721-0.4386-0.22420.6239-0.4002-0.20250.18140.46060.25360.09790.4451-0.28160.8179
184.7384-1.63821.73890.8029-0.97112.00490.7398-0.2461.03131.153-1.75111.69121.2781-0.04430.55970.8508-0.05860.01090.4719-0.57091.3184
191.2401-0.7504-0.12080.45120.09041.95320.03810.4699-0.08490.2963-0.49910.24420.5106-0.240.43950.4241-0.0528-0.0030.3254-0.33110.8713
205.4782-1.0826-5.12831.33750.64085.30461.3443-0.60581.485-0.02231.1840.6482-1.1737-0.2687-0.4487-0.246-0.0669-0.82190.4891-0.3537-0.0829
215.2063-1.6539-2.73863.37322.10742.2405-0.2595-0.4885-0.0725-0.0828-0.12140.63150.17970.17310.2460.41430.0599-0.10990.3365-0.28340.4636
220.42290.64010.20411.23170.37710.95070.08530.29460.6101-0.5049-0.4155-0.3169-0.5163-0.21070.15480.09720.0078-0.15170.7596-0.06180.3423
235.53612.5875-1.41784.85925.20369.27971.88750.77110.47840.78620.5607-2.24110.0749-1.9267-1.61030.13080.16540.32630.4361-0.01850.6484
248.7215-4.838-4.07393.73263.68954.0703-0.3717-1.74130.99340.42110.7245-0.77220.20880.6626-0.45720.5041-0.0429-0.23480.7969-0.25830.4876
253.02062.04412.12846.85515.23877.30070.54930.5593-0.24270.4267-0.62730.82450.45221.3003-0.45150.9681-0.11750.17540.7453-0.55320.6446
262.30530.96981.61870.88770.24386.27090.49960.2967-0.3788-0.05430.3412-0.32710.67190.8416-0.78110.34390.0413-0.00180.7461-0.28390.381
270.6813-0.97440.48521.01270.11722.06510.15140.18580.53560.244-0.5821-0.2661-0.11540.5608-0.2367-0.01180.08930.130.432-0.20170.2872
282.97421.92513.81933.53443.78385.98430.23390.36040.2552-0.22510.1669-0.22140.04820.5046-0.24390.39890.09860.03310.6796-0.3210.5088
Refinement TLS groupSelection details: chain D resid 120:151

+
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