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- PDB-5zct: The crystal structure of the poly-alpha-L-glutamate peptides synt... -

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Basic information

Entry
Database: PDB / ID: 5zct
TitleThe crystal structure of the poly-alpha-L-glutamate peptides synthetase RimK at 2.05 angstrom resolution.
ComponentsRibosomal protein S6--L-glutamate ligase
KeywordsLIGASE / L-amino acid ligase
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 / metal ion binding / identical protein 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, subdomain 1 / ATP-grasp fold, B domain ...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, subdomain 1 / ATP-grasp fold, B domain / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Ribosomal protein bS6--L-glutamate ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsArimura, Y. / Kono, T. / Kino, K. / Kurumizaka, H.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Structural polymorphism of the Escherichia coli poly-alpha-L-glutamate synthetase RimK
Authors: Arimura, Y. / Kono, T. / Kino, K. / Kurumizaka, H.
History
DepositionFeb 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal protein S6--L-glutamate ligase
B: Ribosomal protein S6--L-glutamate ligase
C: Ribosomal protein S6--L-glutamate ligase
D: Ribosomal protein S6--L-glutamate ligase
E: Ribosomal protein S6--L-glutamate ligase
F: Ribosomal protein S6--L-glutamate ligase
G: Ribosomal protein S6--L-glutamate ligase
H: Ribosomal protein S6--L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,42338
Polymers264,8348
Non-polymers5,58930
Water21,3661186
1
A: Ribosomal protein S6--L-glutamate ligase
B: Ribosomal protein S6--L-glutamate ligase
C: Ribosomal protein S6--L-glutamate ligase
D: Ribosomal protein S6--L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,30820
Polymers132,4174
Non-polymers2,89116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17380 Å2
ΔGint-258 kcal/mol
Surface area41960 Å2
MethodPISA
2
E: Ribosomal protein S6--L-glutamate ligase
F: Ribosomal protein S6--L-glutamate ligase
G: Ribosomal protein S6--L-glutamate ligase
H: Ribosomal protein S6--L-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,11518
Polymers132,4174
Non-polymers2,69814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16840 Å2
ΔGint-261 kcal/mol
Surface area42960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.618, 121.628, 119.741
Angle α, β, γ (deg.)90.000, 118.740, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ribosomal protein S6--L-glutamate ligase / Polyglutamate synthase / Ribosomal protein S6 modification protein


Mass: 33104.254 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rimK, b0852, JW0836 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0C0U4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1186 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Bis-Tris propane (pH 7.0), 210 mM Na2SO4, and 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 164792 / % possible obs: 98.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 34.65 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.033 / Rrim(I) all: 0.08 / Χ2: 1.004 / Net I/σ(I): 7.2 / Num. measured all: 875207
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.124.10.55164180.5570.2990.6290.5998.8
2.12-2.214.70.462165820.7520.2320.5190.60599.5
2.21-2.314.10.297150810.9220.1540.3361.34490.7
2.31-2.434.90.27165620.9230.1320.3010.6999.6
2.43-2.585.40.205165890.9640.0950.2260.73899.7
2.58-2.785.60.149166750.9820.0680.1640.81999.8
2.78-3.065.60.104166080.9910.0470.1140.93799.8
3.06-3.516.20.073166800.9960.0310.081.14499.9
3.51-4.426.10.055166680.9970.0240.061.45599.6
4.42-506.40.046169290.9980.020.051.42499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.59 Å48.21 Å
Translation8.59 Å48.21 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IWX

4iwx


Resolution: 2.05→48.213 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.73
RfactorNum. reflection% reflection
Rfree0.2398 8436 5.14 %
Rwork0.196 --
obs0.1983 164146 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.85 Å2 / Biso mean: 42.3758 Å2 / Biso min: 17.94 Å2
Refinement stepCycle: final / Resolution: 2.05→48.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17697 0 326 1186 19209
Biso mean--51.08 42.96 -
Num. residues----2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818265
X-RAY DIFFRACTIONf_angle_d1.06724750
X-RAY DIFFRACTIONf_chiral_restr0.0562892
X-RAY DIFFRACTIONf_plane_restr0.0063173
X-RAY DIFFRACTIONf_dihedral_angle_d10.77611111
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.07330.33052720.28714957522994
2.0733-2.09770.32092820.28355201548399
2.0977-2.12330.31062920.26585195548799
2.1233-2.15020.28232880.24525287557599
2.1502-2.17850.29722700.243952535523100
2.1785-2.20830.27542790.241552195498100
2.2083-2.23990.48742760.38954399467585
2.2399-2.27330.56952190.51024078429777
2.2733-2.30880.28462810.2255248552999
2.3088-2.34670.2622930.22215243553699
2.3467-2.38710.2892750.217752315506100
2.3871-2.43060.27882730.215352985571100
2.4306-2.47730.27622600.211352595519100
2.4773-2.52790.25962900.20551935483100
2.5279-2.58280.25212730.204452965569100
2.5828-2.64290.26673150.204352455560100
2.6429-2.7090.24552840.197152995583100
2.709-2.78220.25872940.202652765570100
2.7822-2.86410.25442650.218352235488100
2.8641-2.95650.28632690.215253035572100
2.9565-3.06220.27352870.207352955582100
3.0622-3.18480.26413050.206552515556100
3.1848-3.32970.25163170.201652535570100
3.3297-3.50520.233040.190552645568100
3.5052-3.72470.25032860.18955239552599
3.7247-4.01220.19432820.171352785560100
4.0122-4.41570.17683140.149752815595100
4.4157-5.0540.17832640.146153605624100
5.054-6.36520.19752600.173453605620100
6.3652-48.22660.16632670.151954265693100

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