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- PDB-5z01: Native Escherichia coli L,D-carboxypeptidase A (LdcA) -

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Basic information

Entry
Database: PDB / ID: 5z01
TitleNative Escherichia coli L,D-carboxypeptidase A (LdcA)
ComponentsMurein tetrapeptide carboxypeptidase
KeywordsHYDROLASE / peptidoglycan / recycling / cell-wall
Function / homology
Function and homology information


glycopeptide catabolic process / muramoyltetrapeptide carboxypeptidase activity / muramoyltetrapeptide carboxypeptidase / peptidoglycan turnover / peptidoglycan biosynthetic process / carboxypeptidase activity / serine-type peptidase activity / cell wall organization / regulation of cell shape / proteolysis / cytosol
Similarity search - Function
Peptidase family S66 / LD-carboxypeptidase A, C-terminal domain superfamily / Murein tetrapeptide carboxypeptidase, N-terminal / LD-carboxypeptidase, N-terminal / LD-carboxypeptidase, C-terminal / LD-carboxypeptidase N-terminal domain / LD-carboxypeptidase C-terminal domain / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
Murein tetrapeptide carboxypeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMeyer, K. / Tame, J.R.H.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: The crystal structure and oligomeric form of Escherichia colil,d-carboxypeptidase A.
Authors: Meyer, K. / Addy, C. / Akashi, S. / Roper, D.I. / Tame, J.R.H.
History
DepositionDec 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Murein tetrapeptide carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7122
Polymers35,6881
Non-polymers241
Water3,819212
1
A: Murein tetrapeptide carboxypeptidase
hetero molecules

A: Murein tetrapeptide carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4244
Polymers71,3752
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3540 Å2
ΔGint-24 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.949, 89.069, 93.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Murein tetrapeptide carboxypeptidase / LD-carboxypeptidase A / Muramoyltetrapeptide carboxypeptidase


Mass: 35687.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ldcA, ycgQ, b1192, JW1181 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P76008, muramoyltetrapeptide carboxypeptidase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.02M Tris pH 8.5, 0.2M sodium thiocyanate, 12% PEG 3350

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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 PILATUS 300K / Detector: PIXEL / Date: May 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→46.9 Å / Num. obs: 33235 / % possible obs: 99.9 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.4
Reflection shellResolution: 1.75→1.77 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.016 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1801 / CC1/2: 0.889 / Rpim(I) all: 0.37 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.886 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.157 / SU B: 3.601 / SU ML: 0.104 / Average fsc free: 0.8431 / Average fsc work: 0.8508 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 1631 4.905 %RANDOM
Rwork0.1762 31620 --
all0.179 ---
obs0.179 33251 99.946 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.459 Å2
Baniso -1Baniso -2Baniso -3
1-4.444 Å20 Å20 Å2
2---1.687 Å20 Å2
3----2.756 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 1 212 2584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192425
X-RAY DIFFRACTIONr_bond_other_d0.0020.022240
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.9493298
X-RAY DIFFRACTIONr_angle_other_deg1.04735171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3225304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02923.304112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91615390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0321519
X-RAY DIFFRACTIONr_chiral_restr0.1120.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212730
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02509
X-RAY DIFFRACTIONr_nbd_refined0.2060.2898
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.24412
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22396
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22416
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2328
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.229
X-RAY DIFFRACTIONr_nbd_other0.2750.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.213
X-RAY DIFFRACTIONr_mcbond_it2.6722.7351219
X-RAY DIFFRACTIONr_mcbond_other2.6712.7331218
X-RAY DIFFRACTIONr_mcangle_it3.5644.0881522
X-RAY DIFFRACTIONr_mcangle_other3.5654.091523
X-RAY DIFFRACTIONr_scbond_it3.7853.2071206
X-RAY DIFFRACTIONr_scbond_other3.7833.2081206
X-RAY DIFFRACTIONr_scangle_it5.7144.6521776
X-RAY DIFFRACTIONr_scangle_other5.7114.6531776
X-RAY DIFFRACTIONr_lrange_it7.24433.9052728
X-RAY DIFFRACTIONr_lrange_other7.17533.5862681
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.75-1.7950.3761250.3323090.33324350.5120.50599.95890.3
1.795-1.8450.2921200.31222380.31123580.5280.521000.279
1.845-1.8980.2981010.28721890.28822920.6760.65999.91270.25
1.898-1.9560.3031080.2521370.25322450.7980.7941000.212
1.956-2.020.277910.20820640.2121580.8640.88299.8610.175
2.02-2.0910.2271040.19220190.19421230.9090.9121000.162
2.091-2.170.2491030.18119010.18520050.90.92299.95010.155
2.17-2.2580.2471080.17118540.17519620.9070.931000.144
2.258-2.3580.1821050.16217960.16319040.9410.94299.84240.135
2.358-2.4730.2940.14916930.15217880.9480.9699.94410.126
2.473-2.6070.196870.14316330.14617200.9490.961000.123
2.607-2.7640.229830.16315280.16616110.9370.9531000.143
2.764-2.9540.248920.15414400.15915330.9320.95699.93480.139
2.954-3.190.184660.17513630.17614290.9570.9551000.163
3.19-3.4930.221620.16712710.1713330.9540.9631000.16
3.493-3.9020.218380.15711660.15812050.9470.96999.9170.154
3.902-4.5010.162390.13310350.13410740.9660.9761000.134
4.501-5.50.183460.1498660.1519120.9680.9751000.151
5.5-7.7250.254440.1796900.1837340.9280.9551000.182
7.725-46.8860.186150.1774280.1774450.9470.95899.55060.189

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