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- PDB-4iwx: Rimk structure at 2.85A -

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Basic information

Entry
Database: PDB / ID: 4iwx
TitleRimk structure at 2.85A
ComponentsRibosomal protein S6 modification proteinRibosome
KeywordsLIGASE / ATP-grasp fold
Function / homology
Function and homology information


ribosomal S6-glutamic acid ligase activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / SOS response / protein modification process / translation / ATP binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein S6--L-glutamate ligase RimK / RimK, PreATP-grasp domain / RimK PreATP-grasp domain / Ribosomal S6 modification enzyme RimK/Lysine biosynthesis enzyme LysX / 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 ...Ribosomal protein S6--L-glutamate ligase RimK / RimK, PreATP-grasp domain / RimK PreATP-grasp domain / Ribosomal S6 modification enzyme RimK/Lysine biosynthesis enzyme LysX / 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 / 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
ADENOSINE-5'-DIPHOSPHATE / GLUTAMIC ACID / Ribosomal protein bS6--L-glutamate ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.854 Å
AuthorsShi, D. / Zhao, G. / Jin, Z. / Allewell, N.M. / Tuchman, M.
CitationJournal: Proteins / Year: 2013
Title: Structure and function of Escherichia coli RimK, an ATP-grasp fold, l-glutamyl ligase enzyme.
Authors: Zhao, G. / Jin, Z. / Wang, Y. / Allewell, N.M. / Tuchman, M. / Shi, D.
History
DepositionJan 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal protein S6 modification protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7068
Polymers34,6511
Non-polymers1,0557
Water181
1
A: Ribosomal protein S6 modification protein
hetero molecules

A: Ribosomal protein S6 modification protein
hetero molecules

A: Ribosomal protein S6 modification protein
hetero molecules

A: Ribosomal protein S6 modification protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,82232
Polymers138,6034
Non-polymers4,21928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
crystal symmetry operation12_565x,x-y+1,-z+2/31
Buried area19590 Å2
ΔGint-409 kcal/mol
Surface area43100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.802, 129.802, 171.239
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-407-

SO4

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Components

#1: Protein Ribosomal protein S6 modification protein / Ribosome


Mass: 34650.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0852, JW0836, rimK / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C0U4
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 6 Å3/Da / Density % sol: 79.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, and 1.8 M ammonium sulfate , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 30431 / Num. obs: 20166 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.85-2.98.40.639188.7
2.9-2.959.50.596191.6
2.95-3.0111.20.565196.6
3.01-3.0713.20.502197.8
3.07-3.1415.30.4971100
3.14-3.2116.80.4431100
3.21-3.2917.50.361100
3.29-3.3817.70.2891100
3.38-3.4817.60.2731100
3.48-3.5917.60.212199.9
3.59-3.7217.50.1921100
3.72-3.8717.50.1441100
3.87-4.0417.40.1271100
4.04-4.2617.40.0941100
4.26-4.5217.20.0891100
4.52-4.87170.0891100
4.87-5.3616.90.081100
5.36-6.1416.80.0751100
6.14-7.7316.30.061199.9
7.73-5014.40.053199.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
DENZOdata reduction
SHELXSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IWY

4iwy


Resolution: 2.854→46.986 Å / Occupancy max: 1 / Occupancy min: 0.34 / SU ML: 0.42 / σ(F): 1.34 / Phase error: 29.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2565 999 4.98 %
Rwork0.2162 --
obs0.2181 20062 98.11 %
all-20448 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.2325 Å2
Refinement stepCycle: LAST / Resolution: 2.854→46.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 62 1 2292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012345
X-RAY DIFFRACTIONf_angle_d1.4753180
X-RAY DIFFRACTIONf_dihedral_angle_d17.386886
X-RAY DIFFRACTIONf_chiral_restr0.097366
X-RAY DIFFRACTIONf_plane_restr0.009407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.854-3.00440.40191280.32152429X-RAY DIFFRACTION90
3.0044-3.19260.34441380.28752671X-RAY DIFFRACTION99
3.1926-3.43910.32531420.25732726X-RAY DIFFRACTION100
3.4391-3.7850.26681420.22062716X-RAY DIFFRACTION99
3.785-4.33240.26361450.18672756X-RAY DIFFRACTION100
4.3324-5.4570.17651480.17432799X-RAY DIFFRACTION100
5.457-46.99260.25411560.22252966X-RAY DIFFRACTION99
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)
13.6669-2.55020.1573.3692-1.27613.1749-0.1093-0.22170.00260.09910.18460.0201-0.25130.1826-0.09480.3849-0.0588-0.02790.4364-0.04730.4084-18.838874.245573.7926
22.9464-2.26571.84674.8873-1.20413.39640.1806-0.21760.4494-0.7466-0.1907-0.0973-0.37150.23940.06440.5876-0.02-0.00280.4319-0.03820.4838-3.535556.109459.8183
32.81392.8434-0.03943.77440.41324.20490.13310.1776-0.4416-0.61840.25370.12680.02840.147-0.32110.47120.0317-0.04880.3833-0.02340.5164-15.167242.849254.8023
40.6218-0.8247-0.31692.51620.60924.20760.0293-0.0645-0.31660.0055-0.00390.18330.4418-0.175-0.08880.4513-0.0271-0.07550.6990.01190.5699-6.375551.528775.1133
56.99520.0995-1.30352.145-1.45296.1593-0.288-0.11440.00250.95950.7121-1.5364-0.83720.5831-0.59170.5404-0.0055-0.04540.6513-0.16170.5982-6.096872.276981.9804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -1:99)
2X-RAY DIFFRACTION2(chain A and resid 100:115)
3X-RAY DIFFRACTION3(chain A and resid 116:180)
4X-RAY DIFFRACTION4(chain A and resid 181:276)
5X-RAY DIFFRACTION5(chain A and resid 277:292)

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