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- PDB-6muq: 1.67 Angstrom Resolution Crystal Structure of Murein-DD-endopepti... -

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Basic information

Entry
Database: PDB / ID: 6muq
Title1.67 Angstrom Resolution Crystal Structure of Murein-DD-endopeptidase from Yersinia enterocolitica.
ComponentsMurein-DD-endopeptidase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / D-ALANYL-D-ALANINE ENDOPEPTIDASE.
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape
Similarity search - Function
Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
ACETATE ION / Murein-DD-endopeptidase
Similarity search - Component
Biological speciesYersinia enterocolitica subsp. palearctica serotype O:3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.67 Angstrom Resolution Crystal Structure of Murein-DD-endopeptidase from Yersinia enterocolitica.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Murein-DD-endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7553
Polymers31,6001
Non-polymers1552
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.201, 37.858, 59.577
Angle α, β, γ (deg.)90.00, 115.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Murein-DD-endopeptidase


Mass: 31599.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica subsp. palearctica serotype O:3 (strain DSM 13030 / CIP 106945 / Y11) (bacteria)
Strain: DSM 13030 / CIP 106945 / Y11 / Gene: Y11_17941 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: A0A0H3NPR7
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1.75 Å3/Da / Density % sol: 29.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7.5 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PEG's II (D1), 0.1M Sodium acetate, 0.1M HEPES (pH 7.5), 22% (w/v) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2018 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.67→30 Å / Num. obs: 26136 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.039 / Rrim(I) all: 0.083 / Rsym value: 0.072 / Χ2: 1.528 / Net I/σ(I): 22.4
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2 / Num. unique obs: 1296 / CC1/2: 0.766 / Rpim(I) all: 0.395 / Rrim(I) all: 0.814 / Rsym value: 0.709 / Χ2: 1.005 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AZI

6azi


Resolution: 1.67→29.83 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.958 / SU B: 6.919 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20354 1283 4.9 %RANDOM
Rwork0.16922 ---
obs0.17091 24714 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.818 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-2.31 Å2
2--0.06 Å20 Å2
3---0.89 Å2
Refinement stepCycle: 1 / Resolution: 1.67→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 9 178 2249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132209
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172114
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.6573003
X-RAY DIFFRACTIONr_angle_other_deg0.4091.5714908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0015288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.02422.079101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.52115354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5831514
X-RAY DIFFRACTIONr_chiral_restr0.0620.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0510.022488
X-RAY DIFFRACTIONr_gen_planes_other0.0470.02442
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2712.0441126
X-RAY DIFFRACTIONr_mcbond_other1.2652.041124
X-RAY DIFFRACTIONr_mcangle_it1.943.0511422
X-RAY DIFFRACTIONr_mcangle_other1.943.0541423
X-RAY DIFFRACTIONr_scbond_it1.7192.3311083
X-RAY DIFFRACTIONr_scbond_other1.7172.3211080
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7273.3861576
X-RAY DIFFRACTIONr_long_range_B_refined5.53625.6022443
X-RAY DIFFRACTIONr_long_range_B_other5.47125.1382407
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 91 -
Rwork0.329 1805 -
obs--99.68 %
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)
13.7202-0.6691-2.19983.2259-0.92591.90810.12190.1087-0.00180.6540.15330.6544-0.4316-0.2806-0.27520.33510.19460.110.536-0.11630.368115.956926.076921.3286
21.3467-0.35160.1962.20530.83292.2223-0.0676-0.0339-0.0891-0.2243-0.01090.1506-0.07410.11320.07850.0492-0.0181-0.0020.08740.00610.021340.445113.704513.4923
31.567-0.5567-0.62562.15170.76891.2888-0.01820.30630.1261-0.58-0.09420.2428-0.30860.00250.11240.2165-0.0086-0.10680.11070.02930.062234.118221.07443.9908
41.69271.9739-0.08234.6974-0.19630.4756-0.08780.0990.2219-0.1925-0.1290.7004-0.2353-0.22710.21690.14620.1154-0.15340.1556-0.15530.239422.169922.675412.2979
52.9509-1.2432-3.24057.3298-1.9965.2911-0.05680.2229-0.1186-0.59250.07040.55070.2833-0.4255-0.01360.14790.0914-0.16090.1552-0.13980.19410.934821.302711.256
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 70
2X-RAY DIFFRACTION2A71 - 219
3X-RAY DIFFRACTION3A220 - 256
4X-RAY DIFFRACTION4A257 - 288
5X-RAY DIFFRACTION5A289 - 310

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