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- PDB-5tv7: 2.05 Angstrom Resolution Crystal Structure of Peptidoglycan-Bindi... -

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Basic information

Entry
Database: PDB / ID: 5tv7
Title2.05 Angstrom Resolution Crystal Structure of Peptidoglycan-Binding Protein from Clostridioides difficile in Complex with Glutamine Hydroxamate.
ComponentsPutative peptidoglycan-binding/hydrolysing protein
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Peptidoglycan-Binding Protein / Glutamine Hydroxamate
Function / homology: / Putative peptidoglycan-binding domain / PGBD superfamily / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / GLUTAMINE HYDROXAMATE / Peptidoglycan-binding/hydrolysing protein
Function and homology information
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsMinasov, G. / Wawrzak, Z. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.05 Angstrom Resolution Crystal Structure of Peptidoglycan-Binding Protein from Clostridioides difficile in Complex with Glutamine Hydroxamate.
Authors: Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative peptidoglycan-binding/hydrolysing protein
B: Putative peptidoglycan-binding/hydrolysing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8234
Polymers39,4992
Non-polymers3242
Water3,621201
1
A: Putative peptidoglycan-binding/hydrolysing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9122
Polymers19,7501
Non-polymers1621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative peptidoglycan-binding/hydrolysing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9122
Polymers19,7501
Non-polymers1621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.949, 35.008, 101.533
Angle α, β, γ (deg.)90.00, 126.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative peptidoglycan-binding/hydrolysing protein


Mass: 19749.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria)
Strain: 630 / Gene: CD630_23880 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Magic / References: UniProt: Q181X4
#2: Chemical ChemComp-HGA / GLUTAMINE HYDROXAMATE


Mass: 162.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 7.8 mg/ml, 0.25M Sodium chloride, 0.01M Tris HCl (pH 8.3), Screen: JCSG+ (B3), 0.1M Bicine (pH 8.5), 20% (w/v) PEG 6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2014 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→29.08 Å / Num. obs: 24487 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 28.1
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 2.06 / CC1/2: 0.769 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→29.08 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 9.416 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.151 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 1199 4.9 %RANDOM
Rwork0.17155 ---
obs0.17346 23265 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.198 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å20 Å21.15 Å2
2---2.9 Å20 Å2
3----0.98 Å2
Refinement stepCycle: 1 / Resolution: 2.05→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 22 201 2683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022600
X-RAY DIFFRACTIONr_bond_other_d0.0010.022435
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.993529
X-RAY DIFFRACTIONr_angle_other_deg0.81735648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6365330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.86425.676111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.91615434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.577158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.022988
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02558
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_it1.4443.271308
X-RAY DIFFRACTIONr_mcbond_other1.4413.271308
X-RAY DIFFRACTIONr_mcangle_it2.4254.8781642
X-RAY DIFFRACTIONr_mcangle_other2.4254.8791643
X-RAY DIFFRACTIONr_scbond_it1.6423.5441292
X-RAY DIFFRACTIONr_scbond_other1.6373.5451292
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7155.2231888
X-RAY DIFFRACTIONr_long_range_B_refined6.11440.0192930
X-RAY DIFFRACTIONr_long_range_B_other5.99239.4992895
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 88 -
Rwork0.279 1627 -
obs--98.11 %
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)
15.4448-0.56831.75134.71211.43545.60770.25240.55760.3723-0.3654-0.1630.588-0.674-0.5504-0.08940.14120.11570.02220.18510.10160.157914.607544.3214-1.0287
25.02110.94530.89796.49334.01668.95190.0520.40620.356-0.22940.21470.6791-0.5342-0.35-0.26670.05280.06230.01020.15730.08280.174213.186942.5863-2.9373
34.5984-2.419-0.11646.4316-1.14152.56780.1136-0.19730.0520.0764-0.10490.216-0.1368-0.129-0.00870.06730.00130.05670.0644-0.01340.059717.082537.816112.8014
42.7985-0.0594-0.92823.55490.33972.6670.0650.0964-0.0081-0.0195-0.10340.03060.0366-0.02180.03840.0097-0.00760.01250.07390.00370.034726.516133.8734.3873
59.3837-1.00242.67842.44070.23562.90150.0260.2898-0.81-0.3709-0.01410.10990.2572-0.0553-0.01190.1459-0.01810.02140.0205-0.04150.09450.145315.040321.4529
69.9805-3.9068-0.25466.8422-0.39275.4437-0.0850.07410.2027-0.28250.05270.4771-0.2693-0.45160.03230.1169-0.0013-0.07880.1255-0.02980.1047-8.24724.236122.2298
73.57871.0971-0.25844.63240.85093.62270.02120.1467-0.2253-0.3159-0.10150.00880.0925-0.06690.08030.10850.03290.03120.08850.00370.03378.826322.029522.1866
82.2545-0.4691-0.02673.47340.35263.29030.0327-0.02480.015-0.045-0.1090.004-0.0268-0.07930.07630.0609-0.0040.01110.07530.00780.00585.677427.73632.8685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 72
2X-RAY DIFFRACTION2A73 - 93
3X-RAY DIFFRACTION3A94 - 128
4X-RAY DIFFRACTION4A129 - 200
5X-RAY DIFFRACTION5B43 - 64
6X-RAY DIFFRACTION6B65 - 86
7X-RAY DIFFRACTION7B87 - 129
8X-RAY DIFFRACTION8B130 - 200

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