[English] 日本語
Yorodumi
- PDB-5i47: Crystal structure of RimK domain protein ATP-grasp from Sphaeroba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i47
TitleCrystal structure of RimK domain protein ATP-grasp from Sphaerobacter thermophilus DSM 20745
ComponentsRimK domain protein ATP-grasp
KeywordsBIOSYNTHETIC PROTEIN / Midwest Center for Structural Genomics / MCSG / putative lysine biosynthesis enzyme / PSI-Biology
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 ...ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RimK domain protein ATP-grasp
Similarity search - Component
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsChang, C. / Duke, N. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115586 United States
CitationJournal: To Be Published
Title: Crystal structure of RimK domain protein ATP-grasp from Sphaerobacter thermophilus DSM 20745
Authors: Chang, C. / Duke, N. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionFeb 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RimK domain protein ATP-grasp
B: RimK domain protein ATP-grasp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5163
Polymers58,4242
Non-polymers921
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-21 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.641, 64.819, 160.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein RimK domain protein ATP-grasp


Mass: 29211.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / S 6022 / Gene: Sthe_0213 / Plasmid: pMCSG7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D1C6B4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Ammonium sulfate, Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 5, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 27874 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 27.32 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Rrim(I) all: 0.077 / Χ2: 0.879 / Net I/av σ(I): 25.559 / Net I/σ(I): 9.1 / Num. measured all: 191899
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.3960.71513380.830.3050.7790.83296.4
2.39-2.436.20.59213360.9050.250.6450.8397.6
2.43-2.486.40.53513510.9170.2250.5820.86298.1
2.48-2.536.60.49113510.9280.2050.5330.8599.5
2.53-2.596.80.47813900.9410.1970.5180.842100
2.59-2.6570.46613610.950.190.5040.818100
2.65-2.717.10.34714090.9760.1410.3750.855100
2.71-2.797.10.30513460.9780.1230.3290.86100
2.79-2.877.10.25113920.9870.1020.2710.903100
2.87-2.967.20.18813800.9890.0760.2030.924100
2.96-3.077.10.16113880.990.0650.1740.916100
3.07-3.197.10.12613790.9930.0510.1360.908100
3.19-3.337.10.08814090.9960.0360.0950.91100
3.33-3.517.20.07413970.9960.030.080.944100
3.51-3.737.20.05613880.9970.0220.0610.933100
3.73-4.027.10.04314110.9980.0170.0470.896100
4.02-4.427.20.03514190.9990.0140.0380.902100
4.42-5.067.10.03214290.9980.0130.0350.838100
5.06-6.3770.03414630.9980.0140.0360.704100
6.37-506.20.03615370.9960.0160.041.04199.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementResolution: 2.35→41.196 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.52 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2386 1940 4.85 %
Rwork0.2009 38057 -
obs0.2028 23363 76.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.28 Å2 / Biso mean: 43.0542 Å2 / Biso min: 8.79 Å2
Refinement stepCycle: final / Resolution: 2.35→41.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3786 0 6 118 3910
Biso mean--52.87 33.33 -
Num. residues----522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033854
X-RAY DIFFRACTIONf_angle_d0.5315253
X-RAY DIFFRACTIONf_chiral_restr0.044648
X-RAY DIFFRACTIONf_plane_restr0.004691
X-RAY DIFFRACTIONf_dihedral_angle_d15.3752328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3496-2.40840.3225600.22031268132835
2.4084-2.47350.2677850.221528161343
2.4735-2.54620.3337790.2271762184149
2.5462-2.62840.25551120.24711946205855
2.6284-2.72230.2213850.2482210229561
2.7223-2.83130.31011260.25522453257969
2.8313-2.96010.24561340.24972724285877
2.9601-3.11620.31721220.25483177329987
3.1162-3.31130.29041340.24233323345793
3.3113-3.56680.29081930.22153485367898
3.5668-3.92550.23011570.183436173774100
3.9255-4.4930.22222270.155835043731100
4.493-5.65830.1762300.157935113741100
5.6583-41.20210.21141960.178135493745100
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)
10.03940.01060.00690.05250.01810.0538-0.0330.10550.1027-0.1336-0.0621-0.1115-0.1190.1296-0.03390.1219-0.03060.00210.16470.02750.187242.092634.81132.4761
20.01880.01260.041-0.00340.00120.0560.0350.11390.0186-0.3735-0.17410.4092-0.1358-0.1615-0.18770.02390.115-0.54080.2007-0.0340.193316.26830.152423.982
30.0071-0.0022-0.00390.02350.01680.00810.0486-0.01620.0340.0912-0.0710.1683-0.1682-0.04870.00040.15960.0228-0.0420.1612-0.02370.185722.420739.986439.9412
40.0428-0.07570.03430.1478-0.07910.05430.09770.0835-0.0765-0.5221-0.07420.2230.1119-0.08360.00560.29330.0395-0.27080.2027-0.14220.170121.90138.838418.8244
50.00550.0153-0.00230.07820.02970.03010.04720.0680.0309-0.1768-0.04440.0013-0.03220.0158-0.00790.45480.00790.12490.34620.02550.202642.857424.488510.9696
60.0199-0.0025-0.00970.018-0.00890.01870.02790.0767-0.075-0.19920.0329-0.07880.07790.10660.00620.53420.1313-0.06790.1922-0.18020.131434.6531-1.420613.5571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 71 )A2 - 71
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 184 )A72 - 184
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 274 )A185 - 274
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 111 )B2 - 111
5X-RAY DIFFRACTION5chain 'B' and (resid 112 through 168 )B112 - 168
6X-RAY DIFFRACTION6chain 'B' and (resid 169 through 274 )B169 - 274

+
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://pdbjlc1.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