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- PDB-5ceb: Bd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus, K... -

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Basic information

Entry
Database: PDB / ID: 5ceb
TitleBd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus, K38M form
ComponentsBd3459
KeywordsHYDROLASE / transpeptidase
Function / homology
Function and homology information


peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / proteolysis
Similarity search - Function
D-Ala-D-Ala carboxypeptidase C, peptidase S13 / Peptidase S13, D-Ala-D-Ala carboxypeptidase C / D-Ala-D-Ala carboxypeptidase 3 (S13) family / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(bba) Sandwich / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLovering, A.L. / Cadby, I.T. / Lambert, C. / Sockett, R.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J015229/1 United Kingdom
CitationJournal: Nat Commun / Year: 2015
Title: Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus.
Authors: Lambert, C. / Cadby, I.T. / Till, R. / Bui, N.K. / Lerner, T.R. / Hughes, W.S. / Lee, D.J. / Alderwick, L.J. / Vollmer, W. / Sockett, E.R. / Lovering, A.L.
History
DepositionJul 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bd3459
B: Bd3459


Theoretical massNumber of molelcules
Total (without water)98,4072
Polymers98,4072
Non-polymers00
Water5,405300
1
A: Bd3459


Theoretical massNumber of molelcules
Total (without water)49,2031
Polymers49,2031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bd3459


Theoretical massNumber of molelcules
Total (without water)49,2031
Polymers49,2031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.930, 65.040, 73.816
Angle α, β, γ (deg.)63.890, 83.270, 83.200
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 38 - 438 / Label seq-ID: 38 - 438

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Bd3459


Mass: 49203.406 Da / Num. of mol.: 2 / Fragment: Bd3459 / Mutation: K38M, S70A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) (bacteria)
Gene: Bd3459 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q6MHT0, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M potassium thiocyanate, 30% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91739 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91739 Å / Relative weight: 1
ReflectionResolution: 1.93→100 Å / Num. obs: 56655 / % possible obs: 85.7 % / Redundancy: 3.8 % / Rsym value: 0.036 / Net I/σ(I): 16.2
Reflection shellRsym value: 0.0766

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3v39

3v39


Resolution: 1.93→66.11 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.652 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 2881 4.8 %RANDOM
Rwork0.1958 ---
obs0.1976 56655 85.61 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 143.21 Å2 / Biso mean: 44.292 Å2 / Biso min: 18.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å21.28 Å2-0.85 Å2
2--0.56 Å2-0.17 Å2
3----1.62 Å2
Refinement stepCycle: final / Resolution: 1.93→66.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5971 0 0 300 6271
Biso mean---43.89 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.026077
X-RAY DIFFRACTIONr_bond_other_d0.0050.025855
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9568199
X-RAY DIFFRACTIONr_angle_other_deg1.178313503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39825.08250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.898151113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.641522
X-RAY DIFFRACTIONr_chiral_restr0.1030.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026846
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021344
X-RAY DIFFRACTIONr_mcbond_it2.6162.1543076
X-RAY DIFFRACTIONr_mcbond_other2.6152.1543075
X-RAY DIFFRACTIONr_mcangle_it3.5793.2173838
Refine LS restraints NCS

Ens-ID: 1 / Number: 47280 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 221 -
Rwork0.372 3786 -
all-4007 -
obs--78.49 %
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)
11.1439-0.25090.91191.3491-0.02165.0311-0.0035-0.2923-0.08420.16540.13850.13810.2475-0.4104-0.1350.03660.01260.00570.26040.11560.10658.81-16.746-42.132
25.4672-0.5888-0.13191.9737-1.56693.78980.02070.5675-0.0523-0.40480.06340.11020.2147-0.269-0.08410.11560.0142-0.03410.22910.06620.06755.027-6.751-78.335
33.8934-0.162-1.96657.6561-2.47912.2841-0.0062-0.53590.84610.7610.0295-0.1916-0.50370.3243-0.02330.28270.0786-0.04890.327-0.0110.324250.9742.534-68.379
44.0766-0.160.33592.2272-0.89612.30810.02910.4657-0.0076-0.3207-0.05360.12080.1212-0.15250.02440.13120.0290.0040.25920.06750.06859.64-6.108-77.706
51.4397-0.22361.27861.0159-0.18233.3082-0.0605-0.0430.08640.04510.09250.0631-0.1396-0.0916-0.0320.00910.02550.01320.19090.10170.066462.887-12.503-45.576
66.1676-0.02651.54084.0754-0.378610.0412-0.0010.2587-0.518-0.37540.0699-0.15090.32650.1317-0.06890.12040.0350.0270.13110.04340.106164.557-16.088-72.371
71.9092-0.07641.01291.2791-0.57415.9274-0.03130.42280.0007-0.04730.0467-0.0930.14750.4455-0.01540.01410.02510.00990.23280.06030.074978.202-51.636-83.918
84.6198-0.4231-0.35581.27930.8324.6633-0.0929-0.42560.1090.44670.1474-0.1838-0.06930.5271-0.05450.28230.055-0.09640.28520.03250.100984.738-43.085-47.711
93.4281-1.3820.51632.99890.81972.1814-0.1891-0.17230.42130.23570.1205-0.5843-0.00310.41620.06860.2680.0836-0.06650.33960.05920.224483.119-39.164-49.453
102.7193-0.4802-0.14631.307-0.07344.7198-0.01860.25130.22850.1287-0.0075-0.2479-0.43240.51690.02610.0698-0.0183-0.0510.25890.05020.1385.356-47.005-73.288
111.9981-0.05941.21981.4375-0.24383.8969-0.15130.01010.20440.05270.09930.0192-0.3643-0.10120.0520.03860.03420.00190.19190.08650.059569.743-46.564-81.897
127.5457-1.75471.20587.9852-4.06899.7809-0.1097-0.4877-0.36460.4804-0.0654-0.0010.4016-0.15620.17510.25640.05870.03430.16590.06550.052674.776-50.735-50.393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 90
2X-RAY DIFFRACTION2A91 - 146
3X-RAY DIFFRACTION3A147 - 183
4X-RAY DIFFRACTION4A184 - 236
5X-RAY DIFFRACTION5A237 - 423
6X-RAY DIFFRACTION6A424 - 438
7X-RAY DIFFRACTION7B38 - 89
8X-RAY DIFFRACTION8B90 - 148
9X-RAY DIFFRACTION9B167 - 232
10X-RAY DIFFRACTION10B233 - 302
11X-RAY DIFFRACTION11B303 - 426
12X-RAY DIFFRACTION12B427 - 438

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