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- PDB-5opz: Crystal structure of Serratia marcescens L-Ala D-Glu endopeptidas... -

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Basic information

Entry
Database: PDB / ID: 5opz
TitleCrystal structure of Serratia marcescens L-Ala D-Glu endopeptidase ChiX
ComponentsChiX
KeywordsHYDROLASE / L-Ala D-Glu endopeptidase Serratia marcescens chitinase secretion anomalous dispersion Zinc enzyme
Function / homology:
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.34 Å
AuthorsOwen, R.A. / Fyfe, P.K. / Lodge, A. / Biboy, J. / Vollmer, W. / Hunter, W.N. / Sargent, F.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
Wellcome Trust094090 United Kingdom
CitationJournal: Biochem. J. / Year: 2018
Title: Structure and activity of ChiX: a peptidoglycan hydrolase required for chitinase secretion by Serratia marcescens.
Authors: Owen, R.A. / Fyfe, P.K. / Lodge, A. / Biboy, J. / Vollmer, W. / Hunter, W.N. / Sargent, F.
History
DepositionAug 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ChiX
B: ChiX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1365
Polymers30,9692
Non-polymers1663
Water6,395355
1
A: ChiX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5863
Polymers15,4851
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ChiX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5502
Polymers15,4851
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.627, 55.531, 51.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 134
2010B2 - 134

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Components

#1: Protein ChiX


Mass: 15484.649 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Strain: Db10 / Gene: ERS381432_02813,chiX / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A0U7UVX7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M tris HCl pH 7.5 0.14 M trimethylamine-N-oxide 16% (w/v) polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.34→55.53 Å / Num. obs: 50019 / % possible obs: 90.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 6.877 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.052 / Net I/σ(I): 6.7
Reflection shellResolution: 1.34→1.36 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1385 / CC1/2: 0.829 / Rpim(I) all: 0.34 / % possible all: 50.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
Aimless1.9.33data scaling
REFMAC5.8.0124phasing
RefinementResolution: 1.34→51.78 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.519 / SU ML: 0.011 / SU R Cruickshank DPI: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.009 / ESU R Free: 0.008 / SU Rfree Cruickshank DPI: 0.0084 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12013 2470 4.9 %RANDOM
Rwork0.08921 ---
obs0.09083 47549 96.64 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 11.119 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20.07 Å2
2---0.17 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.34→51.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 3 355 2494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192456
X-RAY DIFFRACTIONr_bond_other_d0.0070.022372
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.9433356
X-RAY DIFFRACTIONr_angle_other_deg1.38835405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.64820.164122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79915427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3751544
X-RAY DIFFRACTIONr_chiral_restr0.0940.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212899
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02657
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_it1.0750.8821193
X-RAY DIFFRACTIONr_mcbond_other1.0710.881192
X-RAY DIFFRACTIONr_mcangle_it1.3831.3231528
X-RAY DIFFRACTIONr_mcangle_other1.3831.3251529
X-RAY DIFFRACTIONr_scbond_it1.571.1041263
X-RAY DIFFRACTIONr_scbond_other1.5691.1031263
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9741.5831828
X-RAY DIFFRACTIONr_long_range_B_refined3.2358.8863265
X-RAY DIFFRACTIONr_long_range_B_other2.5718.0743063
X-RAY DIFFRACTIONr_rigid_bond_restr1.49134828
X-RAY DIFFRACTIONr_sphericity_free27.586557
X-RAY DIFFRACTIONr_sphericity_bonded8.25855057
Refine LS restraints NCS

Ens-ID: 1 / Number: 16218 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.34→1.375 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 130 -
Rwork0.189 2691 -
obs--73.98 %

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