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- PDB-7b3n: AmiP amidase-3 from Thermus parvatiensis -

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Basic information

Entry
Database: PDB / ID: 7b3n
TitleAmiP amidase-3 from Thermus parvatiensis
ComponentsCell wall hydrolase
KeywordsHYDROLASE / amidase-3 thermophilic
Function / homology: / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / outer membrane-bounded periplasmic space / metal ion binding / Cell wall hydrolase
Function and homology information
Biological speciesThermus parvatiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.793 Å
AuthorsFreitag-Pohl, S. / Pohl, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council (ERC)685778 United Kingdom
CitationJournal: Protein Sci. / Year: 2023
Title: AmiP from hyperthermophilic Thermus parvatiensis prophage is a thermoactive and ultrathermostable peptidoglycan lytic amidase.
Authors: Jasilionis, A. / Plotka, M. / Wang, L. / Dorawa, S. / Lange, J. / Watzlawick, H. / van den Bergh, T. / Vroling, B. / Altenbuchner, J. / Kaczorowska, A.K. / Pohl, E. / Kaczorowski, T. / ...Authors: Jasilionis, A. / Plotka, M. / Wang, L. / Dorawa, S. / Lange, J. / Watzlawick, H. / van den Bergh, T. / Vroling, B. / Altenbuchner, J. / Kaczorowska, A.K. / Pohl, E. / Kaczorowski, T. / Nordberg Karlsson, E. / Freitag-Pohl, S.
History
DepositionDec 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell wall hydrolase
B: Cell wall hydrolase
C: Cell wall hydrolase
D: Cell wall hydrolase
E: Cell wall hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,55529
Polymers95,9795
Non-polymers2,57624
Water4,504250
1
A: Cell wall hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7116
Polymers19,1961
Non-polymers5155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-25 kcal/mol
Surface area7780 Å2
MethodPISA
2
B: Cell wall hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8656
Polymers19,1961
Non-polymers6705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-25 kcal/mol
Surface area7840 Å2
MethodPISA
3
C: Cell wall hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6155
Polymers19,1961
Non-polymers4194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-25 kcal/mol
Surface area7570 Å2
MethodPISA
4
D: Cell wall hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7846
Polymers19,1961
Non-polymers5885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-26 kcal/mol
Surface area7560 Å2
MethodPISA
5
E: Cell wall hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5816
Polymers19,1961
Non-polymers3855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-25 kcal/mol
Surface area7460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.539, 97.988, 148.723
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Cell wall hydrolase / Cell wall hydrolase/autolysin


Mass: 19195.770 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus parvatiensis (bacteria) / Gene: AV541_09585, RLTM_01600 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H7GE39

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Non-polymers , 7 types, 274 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 0.1 M hepes pH 7.8, 65 % MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.2824 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 1.79→46.53 Å / Num. obs: 86433 / % possible obs: 96.9 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.035 / Rrim(I) all: 0.05 / Χ2: 1.01 / Net I/σ(I): 9.2
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 1.9 % / Rmerge(I) obs: 1.132 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3209 / CC1/2: 0.283 / Rpim(I) all: 1.132 / Rrim(I) all: 1.601 / Χ2: 1.21 / % possible all: 69.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
DIALSdata scaling
SHELXDEphasing
xia2data reduction
AutoSolphasing
autoSHARPphasing
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.793→43.679 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.336 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.119 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 4282 4.96 %Random selection
Rwork0.1848 82055 --
all0.187 ---
obs-86337 96.825 %-
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: 38.893 Å2
Baniso -1Baniso -2Baniso -3
1--0.132 Å2-0 Å20 Å2
2--0.067 Å20 Å2
3---0.064 Å2
Refinement stepCycle: LAST / Resolution: 1.793→43.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6302 0 139 251 6692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136680
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176192
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.6569135
X-RAY DIFFRACTIONr_angle_other_deg1.3931.56714202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1035865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.79417.938354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10615898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4011583
X-RAY DIFFRACTIONr_chiral_restr0.0730.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021586
X-RAY DIFFRACTIONr_nbd_refined0.2120.21459
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.25534
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23259
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22975
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1490.27
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1080.212
X-RAY DIFFRACTIONr_nbd_other0.1910.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.215
X-RAY DIFFRACTIONr_mcbond_it3.1953.9523395
X-RAY DIFFRACTIONr_mcbond_other3.1943.9513394
X-RAY DIFFRACTIONr_mcangle_it4.1895.9124242
X-RAY DIFFRACTIONr_mcangle_other4.195.9134243
X-RAY DIFFRACTIONr_scbond_it4.0984.3943285
X-RAY DIFFRACTIONr_scbond_other4.0494.3833271
X-RAY DIFFRACTIONr_scangle_it5.896.444879
X-RAY DIFFRACTIONr_scangle_other5.8146.4254862
X-RAY DIFFRACTIONr_lrange_it7.45847.977453
X-RAY DIFFRACTIONr_lrange_other7.4647.9767454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.793-1.8390.3672320.3934441X-RAY DIFFRACTION71.7378
1.839-1.890.3442600.3545196X-RAY DIFFRACTION86.3155
1.89-1.9440.3143150.3015795X-RAY DIFFRACTION99.1883
1.944-2.0040.2813090.2525708X-RAY DIFFRACTION99.917
2.004-2.070.2563100.2235534X-RAY DIFFRACTION100
2.07-2.1420.2352760.2015361X-RAY DIFFRACTION99.9823
2.142-2.2230.2122890.1775188X-RAY DIFFRACTION99.9453
2.223-2.3140.2292580.1714976X-RAY DIFFRACTION99.9427
2.314-2.4170.2092470.1634782X-RAY DIFFRACTION99.9801
2.417-2.5350.2072540.1614562X-RAY DIFFRACTION99.9378
2.535-2.6720.2522100.1754403X-RAY DIFFRACTION100
2.672-2.8340.2091970.1634153X-RAY DIFFRACTION99.954
2.834-3.030.1971980.1563912X-RAY DIFFRACTION99.9757
3.03-3.2720.2381670.1613692X-RAY DIFFRACTION99.9741
3.272-3.5840.2031950.1623353X-RAY DIFFRACTION99.9718
3.584-4.0070.2111500.1583062X-RAY DIFFRACTION100
4.007-4.6270.1881590.1562709X-RAY DIFFRACTION99.9651
4.627-5.6650.2241150.1992317X-RAY DIFFRACTION99.8768
5.665-8.0060.251870.2111853X-RAY DIFFRACTION100
8.006-430.246540.2191058X-RAY DIFFRACTION97.6295

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