[English] 日本語
Yorodumi
- PDB-3q6c: X-ray crystal structure of duf2500 (pf10694) from klebsiella pneu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q6c
TitleX-ray crystal structure of duf2500 (pf10694) from klebsiella pneumoniae, northeast structural genomics consortium target kpr96
Componentsprobable receptor YhhM
KeywordsStructure Genomics / unknown function / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / KPK_0280 protein
Function / homology:
Function and homology information
Biological speciesKlebsiella variicola At-22 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsSeetharaman, J. / Su, M. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Seetharaman, J. / Su, M. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-ray crystal structure of duf2500 (pf10694) from klebsiella pneumoniae, northeast structural genomics consortium target kpr96
Authors: Seetharaman, J. / Su, M. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast ...Authors: Seetharaman, J. / Su, M. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
History
DepositionDec 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Structure summary
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: probable receptor YhhM
B: probable receptor YhhM
C: probable receptor YhhM
D: probable receptor YhhM
E: probable receptor YhhM
F: probable receptor YhhM
G: probable receptor YhhM
H: probable receptor YhhM
I: probable receptor YhhM
J: probable receptor YhhM
K: probable receptor YhhM
L: probable receptor YhhM
M: probable receptor YhhM
N: probable receptor YhhM
O: probable receptor YhhM
P: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)151,60716
Polymers151,60716
Non-polymers00
Water6,900383
1
A: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: probable receptor YhhM

N: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)18,9512
Polymers18,9512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_647-x+1,y-1/2,-z+21
Buried area830 Å2
ΔGint-7 kcal/mol
Surface area7980 Å2
MethodPISA
9
I: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
O: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
P: probable receptor YhhM


Theoretical massNumber of molelcules
Total (without water)9,4751
Polymers9,4751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.714, 93.613, 137.340
Angle α, β, γ (deg.)90.00, 97.31, 90.00
Int Tables number4
Space group name H-MP1211
DetailsSLS shows this is a monomer in solution. http://spine.nesg.org/aggregation.cgi?batch_id=KpR96-37-119-21.5-SeMa-GF. But it forms a dimer in crystal structure.

-
Components

#1: Protein
probable receptor YhhM


Mass: 9475.468 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella variicola At-22 (bacteria) / Strain: At-22 / Gene: Kvar_0268 / References: UniProt: D3RD65
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES (pH 7.5), 40% PEG8k, and 0.1M potassium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 74845 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.053
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.39 / Rsym value: 0.38 / % possible all: 88.4

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→49.45 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 54632.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.284 3650 4.9 %RANDOM
Rwork0.225 ---
obs0.242 74845 83.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.708 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å2-0.42 Å2
2--1.47 Å20 Å2
3----1.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8464 0 0 383 8847
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.84
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 445 4.7 %
Rwork0.286 9075 -
obs--63.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

+
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