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- PDB-5nj5: E. coli Microcin-processing metalloprotease TldD/E with phosphate... -

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Basic information

Entry
Database: PDB / ID: 5nj5
TitleE. coli Microcin-processing metalloprotease TldD/E with phosphate bound
Components(Metalloprotease ...Metalloproteinase) x 2
KeywordsHYDROLASE / metalloprotease / microcin / CcdA / DNA gyrase
Function / homology
Function and homology information


peptidase complex / Hydrolases; Acting on peptide bonds (peptidases) / protein processing / metallopeptidase activity / iron ion binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
TldD / Metalloprotease TldD/E, C-terminal domain / Metalloprotease TldD/E, central domain / : / PmbA/TldD fold / PmbA/TldD superfamily / PmbA/TldA metallopeptidase C-terminal domain / Metalloprotease TldD/E, N-terminal domain / Metalloprotease TldD/PmbA, N-terminal / Metalloprotease TldD/PmbA superfamily ...TldD / Metalloprotease TldD/E, C-terminal domain / Metalloprotease TldD/E, central domain / : / PmbA/TldD fold / PmbA/TldD superfamily / PmbA/TldA metallopeptidase C-terminal domain / Metalloprotease TldD/E, N-terminal domain / Metalloprotease TldD/PmbA, N-terminal / Metalloprotease TldD/PmbA superfamily / PmbA/TldA metallopeptidase domain 1 / PmbA/TldA metallopeptidase central domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Metalloprotease PmbA / Metalloprotease TldD
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGhilarov, D. / Serebryakova, M. / Stevenson, C.E.M. / Hearnshaw, S.J. / Volkov, D. / Maxwell, A. / Lawson, D.M. / Severinov, K.
Funding support Russian Federation, Poland, United Kingdom, 6items
OrganizationGrant numberCountry
Dynasty foundationPersonal fellowship Russian Federation
Russian Ministry of ScienceResearch and Scientific-Pedagogical Personnel of Innovative Russia in 2009-2013 grant 8591 Russian Federation
European UnionMarie Sklodowska-Curie grant agreement No. 665778 Poland
Biotechnology and Biological Sciences Research CouncilBB/J016853/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 (MET) United Kingdom
John Innes Foundation United Kingdom
CitationJournal: Structure / Year: 2017
Title: The Origins of Specificity in the Microcin-Processing Protease TldD/E.
Authors: Ghilarov, D. / Serebryakova, M. / Stevenson, C.E.M. / Hearnshaw, S.J. / Volkov, D.S. / Maxwell, A. / Lawson, D.M. / Severinov, K.
History
DepositionMar 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metalloprotease TldD
B: Metalloprotease PmbA
C: Metalloprotease TldD
D: Metalloprotease PmbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,09220
Polymers203,0264
Non-polymers1,06616
Water32,3731797
1
A: Metalloprotease TldD
B: Metalloprotease PmbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,04610
Polymers101,5132
Non-polymers5338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-42 kcal/mol
Surface area33520 Å2
MethodPISA
2
C: Metalloprotease TldD
D: Metalloprotease PmbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,04610
Polymers101,5132
Non-polymers5338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-43 kcal/mol
Surface area33510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.770, 173.990, 83.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUTHRTHRAA3 - 48017 - 494
21LEULEUTHRTHRCC3 - 48017 - 494
12VALVALGLNGLNBB7 - 4507 - 450
22VALVALGLNGLNDD7 - 4507 - 450

NCS ensembles :
ID
1
2

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Components

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Metalloprotease ... , 2 types, 4 molecules ACBD

#1: Protein Metalloprotease TldD


Mass: 53091.551 Da / Num. of mol.: 2 / Mutation: G401D
Source method: isolated from a genetically manipulated source
Details: The TldD protein was expressed with a fourteen residue nickel affinity tag with sequence MGSSHHHHHHSQDP appended to the N-terminus of the full-length amino acid sequence
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: tldD, yhdO, b3244, JW3213 / Plasmid: pCOLADuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star
References: UniProt: P0AGG8, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein Metalloprotease PmbA / Protein TldE


Mass: 48421.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: pmbA, tldE, b4235, JW4194 / Plasmid: pCOLADuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star
References: UniProt: P0AFK0, Hydrolases; Acting on peptide bonds (peptidases)

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Non-polymers , 4 types, 1813 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1797 / 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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.383
11h,-k,-l20.617
ReflectionResolution: 1.9→75.29 Å / Num. obs: 136171 / % possible obs: 94.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.047 / Rrim(I) all: 0.1 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.9530.5510.5650.3920.68369.1
8.5-75.294.60.0270.9990.0140.03199.1

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TV9

3tv9


Resolution: 1.9→75.29 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.966 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.026
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1781 6723 4.9 %RANDOM
Rwork0.1386 ---
obs0.1406 129447 93.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.65 Å2 / Biso mean: 22.126 Å2 / Biso min: 4.27 Å2
Baniso -1Baniso -2Baniso -3
1--9.95 Å20 Å2-0.27 Å2
2--6.61 Å20 Å2
3---3.34 Å2
Refinement stepCycle: final / Resolution: 1.9→75.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13827 0 64 1862 15753
Biso mean--30.9 30.78 -
Num. residues----1847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914556
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213493
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.96719772
X-RAY DIFFRACTIONr_angle_other_deg0.927331293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42251949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81224.392617
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.759152435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.13315100
X-RAY DIFFRACTIONr_chiral_restr0.0830.22234
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216793
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022887
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A30820
12C30820
21B28470
22D28470
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 361 -
Rwork0.194 6996 -
all-7357 -
obs--68.71 %
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)
13.4810.15390.38281.44020.09891.4401-0.0664-0.06750.3006-0.03890.0172-0.0301-0.17210.08880.04920.07510.0117-0.01740.04250.02240.069524.385790.739429.1382
24.0009-2.05381.46061.1948-0.70490.5489-0.0294-0.0448-0.01440.00080.0551-0.0399-0.0092-0.0009-0.02570.02670.0129-0.01910.07770.00490.054641.615375.010639.735
30.8743-0.19640.60470.4625-0.27340.8596-0.05340.07260.2020.0255-0.02-0.0353-0.0830.0820.07340.014-0.0025-0.01060.01310.00730.061434.71578.681340.3874
40.751-0.78060.53351.0155-0.68210.5574-0.0333-0.04580.08460.0782-0.0089-0.0436-0.030.03560.04230.03320.0006-0.0160.0301-0.01910.050743.402472.611654.3819
50.3955-0.03910.02030.6829-0.30570.5253-0.0223-0.09560.04220.08960.04310.0378-0.0277-0.0677-0.02080.02280.0175-0.00780.0395-0.01770.018824.290868.276260.4856
65.07741.20091.18831.66510.39691.9336-0.20660.40270.2362-0.22820.11530.1575-0.12180.0760.09140.0368-0.0145-0.01790.0420.01590.057445.584967.586219.987
70.87310.1031-0.0040.1698-0.0370.1902-0.03520.04990.0693-0.01810.01970.0054-0.01090.02530.01550.02060.0061-0.02120.0166-0.00590.024833.26663.972929.7697
83.04690.4511-0.99230.4373-0.18920.3347-0.0012-0.10240.08810.04760.03110.0473-0.00960.0455-0.02990.02040-0.01190.0585-0.00140.026227.147458.519430.3156
91.52930.4619-2.27570.4263-0.77043.4584-0.0483-0.152-0.01380.03620.0769-0.05050.0770.1835-0.02860.01920.0235-0.03420.0691-0.00950.087914.514850.993336.4806
100.80190.1402-0.57770.3219-0.17691.0032-0.0295-0.0373-0.05040.03810.0254-0.01620.0570.04590.00420.02420.013-0.01620.0082-0.00530.02133.861442.54845.5689
114.13620.5163-0.23620.96561.17671.6732-0.08510.1045-0.6010.0357-0.0029-0.01930.1339-0.02710.0880.1058-0.0079-0.03010.02030.01720.16815.9531-3.1818-11.4001
121.5214-0.3238-0.80950.4430.30090.83860.00710.1505-0.2305-0.0353-0.0410.0234-0.0025-0.08320.03390.032-0.0046-0.02930.0164-0.01630.0809-0.74698.7791-9.1981
132.0037-1.729-1.22812.09260.37471.7987-0.1413-0.0456-0.43010.00270.02890.31570.22370.06660.11250.1072-0.0298-0.01630.02140.00670.2932-2.1406-5.29672.3238
141.3374-0.137-0.41714.68153.3563.53020.0980.0207-0.09580.1021-0.16330.15450.1282-0.25830.06530.0208-0.0106-0.01480.04980.02450.048-26.496416.04412.797
150.4409-0.0821-0.0510.47220.24580.3951-0.0179-0.1326-0.09290.09140.0209-0.01990.03320.0515-0.0030.03140.0004-0.02120.04570.0320.04630.607416.061117.0799
169.1863.2485-2.22122.5918-1.0292.1437-0.1590.2095-0.0463-0.20420.1058-0.0653-0.01650.04970.05320.05060.0073-0.02670.0384-0.03310.0478-15.223417.4651-24.0398
170.67270.1277-0.13430.09870.02620.1317-0.0230.0736-0.1066-0.0160.01180.01140.0251-0.02990.01120.0174-0.0055-0.01880.0126-0.00950.0512-12.964419.5512-13.4112
182.22311.09142.15151.60751.27255.3613-0.03630.0405-0.0031-0.03710.0528-0.0405-0.07850.0585-0.01650.01160.0094-0.0010.01380.00110.033321.851526.9714-8.6926
192.15650.36250.68210.2190.19360.2706-0.0338-0.08430.03410.01920.0295-0.0093-0.008-0.01790.00430.02280.0147-0.02190.026-0.00370.037.845130.548-9.4841
200.86660.08390.58380.23830.12720.8547-0.0159-0.07680.04330.04130.015-0.0053-0.0409-0.02050.00090.01690.0041-0.00670.0105-0.00750.0142-3.881442.89463.8733
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 32
2X-RAY DIFFRACTION2A33 - 63
3X-RAY DIFFRACTION3A64 - 158
4X-RAY DIFFRACTION4A159 - 239
5X-RAY DIFFRACTION5A240 - 481
6X-RAY DIFFRACTION6B9 - 42
7X-RAY DIFFRACTION7B43 - 158
8X-RAY DIFFRACTION8B159 - 200
9X-RAY DIFFRACTION9B201 - 233
10X-RAY DIFFRACTION10B234 - 450
11X-RAY DIFFRACTION11C3 - 42
12X-RAY DIFFRACTION12C43 - 107
13X-RAY DIFFRACTION13C108 - 128
14X-RAY DIFFRACTION14C129 - 159
15X-RAY DIFFRACTION15C160 - 481
16X-RAY DIFFRACTION16D9 - 32
17X-RAY DIFFRACTION17D33 - 129
18X-RAY DIFFRACTION18D130 - 161
19X-RAY DIFFRACTION19D162 - 231
20X-RAY DIFFRACTION20D232 - 450

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