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- PDB-6vr7: Structure of a pseudomurein peptide ligase type C from Methanothe... -

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Basic information

Entry
Database: PDB / ID: 6vr7
TitleStructure of a pseudomurein peptide ligase type C from Methanothermus fervidus
ComponentsMur ligase middle domain protein
KeywordsLIGASE / Pseudomurein / pseudomurein peptide ligase / archaeal cell wall / Methanothermus fervidus
Function / homology
Function and homology information


tetrahydrofolylpolyglutamate synthase activity / ATP binding / metal ion binding
Similarity search - Function
Folylpolyglutamate synthase signature 1. / Folylpolyglutamate synthetase, conserved site / Mur ligase, C-terminal domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / Protein-Tyrosine Phosphatase; Chain A ...Folylpolyglutamate synthase signature 1. / Folylpolyglutamate synthetase, conserved site / Mur ligase, C-terminal domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / Protein-Tyrosine Phosphatase; Chain A / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETOACETIC ACID / Mur ligase middle domain protein
Similarity search - Component
Biological speciesMethanothermus fervidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCarbone, V. / Schofield, L.R. / Sutherland-Smith, A.J. / Ronimus, R.S. / Subedi, B.P.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New ZealandAGR1301 New Zealand
CitationJournal: FEMS Microbes / Year: 2021
Title: Archaeal pseudomurein and bacterial murein cell wall biosynthesis share a common evolutionary ancestry
Authors: Subedi, B.P. / Martin, W.F. / Carbone, V. / Duin, E.C. / Cronin, B. / Sauter, J. / Schofield, L.R. / Sutherland-Smith, A.J. / Ronimus, R.S.
History
DepositionFeb 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 2.0Jul 28, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / chem_comp / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet_range / struct_site / struct_site_gen / symmetry
Item: _cell.volume / _chem_comp.formula ..._cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_number_measured_all / _reflns.pdbx_scaling_rejects / _reflns.percent_possible_obs / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _symmetry.space_group_name_Hall
Description: Ligand geometry / Provider: author / Type: Coordinate replacement
Revision 2.1Sep 29, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mur ligase middle domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0137
Polymers54,4701
Non-polymers5446
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-17 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.802, 97.802, 138.351
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mur ligase middle domain protein / Pseudomurein peptide ligase type C


Mass: 54469.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermus fervidus (archaea) / Gene: Mfer_0336 / Plasmid: pET15b_mfer336 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 STAR / References: UniProt: E3GXV7

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Non-polymers , 5 types, 81 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-AAE / ACETOACETIC ACID


Mass: 102.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350, 0.33% w/v 1,5-naphthalenedisulfonic acid disodium salt, 0.33% w/v 2,5-pyridinedicarboxylic acid, 0.33% w/v3,5-dinitrosalicylic ...Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350, 0.33% w/v 1,5-naphthalenedisulfonic acid disodium salt, 0.33% w/v 2,5-pyridinedicarboxylic acid, 0.33% w/v3,5-dinitrosalicylic acid, 0.02 M HEPES sodium, pH 6.8
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9117 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 5, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9117 Å / Relative weight: 1
ReflectionResolution: 2.5→46.11 Å / Num. obs: 23904 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.06 / Rrim(I) all: 0.16 / Net I/σ(I): 13.5 / Num. measured all: 170022 / Scaling rejects: 3303
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.67.40.9521955026480.8240.3771.0252.7100
9.01-46.115.90.0335545980.9790.0140.03342.698.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
iMOSFLMdata reduction
Aimlessdata scaling
MoRDaphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4CVK

4cvk


Resolution: 2.5→46.11 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 1173 4.94 %RANDOM
Rwork0.2133 22577 --
obs0.2167 23750 99.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.4 Å2 / Biso mean: 53.662 Å2 / Biso min: 19.41 Å2
Refinement stepCycle: final / Resolution: 2.5→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3725 0 30 75 3830
Biso mean--52.25 37.98 -
Num. residues----485
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.610.32011380.255528012939100
2.61-2.750.43241180.32332759287799
2.75-2.920.38551570.257327822939100
2.92-3.150.33981460.237828122958100
3.15-3.470.30271550.23652771292699
3.47-3.970.26731510.21822745289697
3.97-50.21811610.161528693030100
5-46.110.2291470.176830383185100
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)
10.6117-0.2369-0.27980.58680.26972.73130.0974-0.7037-0.08280.6448-0.24750.31520.1909-0.41770.1380.8355-0.12520.20860.5669-0.05070.399521.9018-1.92365.1794
21.4466-0.12860.25482.9396-0.93821.40220.1030.1188-0.0489-0.0304-0.1070.13720.00740.09620.02530.24760.0265-0.01560.2269-0.06770.300931.09515.798131.3737
31.6431-0.8025-0.44111.75690.04091.09830.05760.0631-0.2566-0.0388-0.04120.33550.1417-0.1005-0.02990.3170.0009-0.05150.2581-0.03260.67817.164618.33629.9951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 107 )A5 - 107
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 347 )A108 - 347
3X-RAY DIFFRACTION3chain 'A' and (resid 348 through 492 )A348 - 492

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