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- PDB-6ov8: 2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B fro... -

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Basic information

Entry
Database: PDB / ID: 6ov8
Title2.6 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str. K-12 substr. MG1655
ComponentsPeptidase B
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Aminopeptidase B
Function / homology
Function and homology information


PepB aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / peptidase activity / manganese ion binding / proteolysis / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Peptidase M17, peptidase B / : / Peptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsMinasov, G. / Shuvalova, L. / Wawrzak, Z. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Citation
Journal: Protein Sci. / Year: 2020
Title: Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis.
Authors: Minasov, G. / Lam, M.R. / Rosas-Lemus, M. / Slawek, J. / Woinska, M. / Shabalin, I.G. / Shuvalova, L. / Palsson, B.O. / Godzik, A. / Minor, W. / Satchell, K.J.F.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structural comparison of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida with PobA from other Pseudomonas spp. and other monooxygenases.
Authors: Lazar, J.T. / Shuvalova, L. / Rosas-Lemus, M. / Kiryukhina, O. / Satchell, K.J.F. / Minasov, G.
#2: Journal: Febs J. / Year: 2020
Title: Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain.
Authors: Shabalin, I.G. / Gritsunov, A. / Hou, J. / Slawek, J. / Miks, C.D. / Cooper, D.R. / Minor, W. / Christendat, D.
History
DepositionMay 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id
Revision 1.2Apr 7, 2021Group: Database references / Category: citation / citation_author
Revision 1.3Oct 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 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: Peptidase B
B: Peptidase B
C: Peptidase B
D: Peptidase B
E: Peptidase B
F: Peptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,01339
Polymers281,5466
Non-polymers1,46733
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, 6OAD
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26730 Å2
ΔGint-637 kcal/mol
Surface area83770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.857, 148.190, 165.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Peptidase B / Aminopeptidase B


Mass: 46924.324 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: pepB, yfhI, b2523, JW2507 / Variant: MG1655 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: P37095, PepB aminopeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 8.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 1mM Zn, 1mM Mn Screen: Classics II (F10), 0.2M Sodium chloride, 0.1M BIS-TRIS pH 5.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2019 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 85965 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.059 / Rrim(I) all: 0.149 / Rsym value: 0.136 / Χ2: 1.19 / Net I/σ(I): 14.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4231 / CC1/2: 0.837 / Rpim(I) all: 0.341 / Rrim(I) all: 0.861 / Rsym value: 0.79 / Χ2: 1.001 / % possible all: 100

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Processing

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

6oad


Resolution: 2.61→29.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.908 / SU B: 22.881 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 2.558 / ESU R Free: 0.314 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 4240 4.9 %RANDOM
Rwork0.1813 ---
obs0.18411 81597 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.039 Å2
Baniso -1Baniso -2Baniso -3
1-3.14 Å20 Å20 Å2
2--1.36 Å20 Å2
3----4.5 Å2
Refinement stepCycle: 1 / Resolution: 2.61→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19510 0 33 614 20157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01319992
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718349
X-RAY DIFFRACTIONr_angle_refined_deg1.0421.6427066
X-RAY DIFFRACTIONr_angle_other_deg0.2911.57842445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.22452570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.81922.2961041
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52153093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.23815139
X-RAY DIFFRACTIONr_chiral_restr0.0420.22618
X-RAY DIFFRACTIONr_gen_planes_refined0.0520.0222938
X-RAY DIFFRACTIONr_gen_planes_other0.0470.024267
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_it0.992.91910280
X-RAY DIFFRACTIONr_mcbond_other0.992.91910279
X-RAY DIFFRACTIONr_mcangle_it1.7084.37612850
X-RAY DIFFRACTIONr_mcangle_other1.7084.37612851
X-RAY DIFFRACTIONr_scbond_it1.1123.0289712
X-RAY DIFFRACTIONr_scbond_other1.1113.0289712
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7964.48814216
X-RAY DIFFRACTIONr_long_range_B_refined3.24534.10721864
X-RAY DIFFRACTIONr_long_range_B_other3.21234.06321800
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.609→2.676 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 304 -
Rwork0.289 5696 -
obs--96.28 %
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)
11.86810.4775-2.11493.4055-1.62882.8054-0.0065-0.1243-0.09030.04090.09410.2660.03320.1441-0.08770.0390.024-0.06770.18960.00020.2521-11.1819-41.5754-20.3188
23.07060.14061.0533.39351.05494.21420.01630.0878-0.0814-0.0422-0.05020.22680.0827-0.20660.03380.0267-0.01070.01070.02580.00950.077-2.6149-40.3235-18.6461
31.10630.48410.11661.36690.011.2212-0.0282-0.1206-0.07850.11950.0210.02960.12110.00430.00720.06320.01340.00560.03030.04250.082120.0548-37.55180.5245
40.7065-0.0941-0.13542.83040.20820.7774-0.0159-0.0588-0.05430.03810.0532-0.06230.08020.0994-0.03730.11750.0114-0.01650.07510.01190.070229.3226-29.9579-5.3304
51.19130.3531-0.18660.89350.1330.64670.04950.0768-0.0678-0.042-0.0040.00940.08040.0281-0.04550.09280.0325-0.00440.04210.01850.066127.9105-32.1774-18.0314
64.22462.59483.94233.96514.44945.4566-0.01310.1024-0.26560.43880.1182-0.13790.40690.202-0.10510.27910.14610.01410.4387-0.07330.49564.0287-20.7724-31.3773
72.6583-1.00441.4071.5122-0.35532.51460.04670.1446-0.0433-0.14830.0781-0.1320.09440.4194-0.12470.0629-0.02760.05550.1546-0.00930.135450.4909-18.3114-42.2433
87.37673.87421.25772.2876-0.63728.0144-0.23480.22320.2616-0.1970.02820.0387-0.07540.29880.20660.24760.04240.09630.15220.12320.190931.7929-18.4872-61.2156
90.7812-0.2663-0.09851.4825-0.07511.08840.02270.06240.0027-0.14580.00520.07310.0183-0.079-0.02790.0838-0.0381-0.00250.06890.02410.044720.0011-17.123-48.4264
101.49160.2414-0.42150.3548-0.2850.8938-0.01450.0031-0.132-0.00040.0171-0.04920.2068-0.0141-0.00260.1337-0.00870.01870.07640.01120.107924.7979-26.4871-37.148
115.85280.96410.35781.12062.55226.578-0.16990.1313-0.0016-0.13530.2208-0.0541-0.11750.5918-0.0510.42510.06270.06760.3697-0.06830.293568.1765-5.969-28.5859
121.3204-0.4252-0.98090.57680.6592.8205-0.0231-0.1053-0.03740.03750.1176-0.2153-0.00020.5335-0.09460.0258-0.0209-0.03440.1412-0.03420.164360.4889-2.9928-9.2401
1318.5876-2.7091-7.16483.74940.12233.69070.1431-0.1943-0.2951-0.0142-0.08170.2083-0.08440.0566-0.06140.15860.0134-0.02950.08770.01870.063336.67512.774417.8033
140.6373-0.1940.15051.29760.22290.4427-0.0364-0.07080.04760.02770.00110.0225-0.21010.02920.03530.1739-0.0353-0.01510.10890.010.097239.42067.5525.66
151.3449-0.2219-0.33851.1343-0.02741.40280.06840.06360.16250.02790.0103-0.1927-0.19060.0461-0.07860.1566-0.0607-0.04260.04080.01430.077741.824114.7627-6.7902
162.5139-0.03580.87482.2631-2.6867.00360.1229-0.1062-0.0887-0.17970.17350.25350.60670.1464-0.29640.0838-0.0098-0.02680.102-0.00920.1879-20.4217-32.6365-20.739
170.45710.5826-0.22692.3677-0.89081.2694-0.02830.0810.0007-0.08810.09950.2260.0213-0.2089-0.07120.00850.0108-0.02360.16030.00410.1186-18.0926-14.379-33.0052
189.74024.4605-1.20749.0685-0.75772.1484-0.33370.2164-0.2331-0.35840.4152-0.43390.2692-0.0168-0.08150.13680.0155-0.01090.16820.03690.0587-3.540814.4353-47.613
190.9199-0.1713-0.24661.05810.34940.7377-0.00310.11560.1482-0.0510.04030.1411-0.1729-0.1263-0.03720.08430.0239-0.01240.09150.07040.1383-6.37939.459-35.112
201.09430.77970.07841.0557-0.05010.56440.0357-0.05830.1810.0779-0.05620.3417-0.1288-0.1930.02040.07740.0512-0.00510.14330.0240.2032-9.8446.2768-21.3141
216.0485-1.2239-3.37683.2044-0.09612.14220.1045-0.1390.12460.53460.0166-0.1764-0.39540.0181-0.12110.74630.1430.18830.18910.03770.56422.719840.1702-0.0101
225.958-0.328-1.80436.9351-3.36283.050.38280.59460.15880.1559-0.22670.2784-0.0715-0.3959-0.15610.24190.10670.07630.27710.03430.2837-1.535233.4714-3.531
230.99610.3282-0.19063.1517-1.11961.02720.0511-0.1740.14470.44370.0343-0.0186-0.1992-0.0939-0.08530.1940.06520.01570.1289-0.04730.05843.140812.749512.9551
241.6652-0.6015-0.12321.82080.58260.5606-0.028-0.2036-0.07370.16110.04080.13320.0264-0.07-0.01280.08060.03930.0250.1290.04080.04820.0277-3.87258.3623
250.69750.01170.27290.7554-0.35730.4652-0.003-0.1083-0.02720.010.03890.2633-0.0429-0.1753-0.03590.04710.06470.01850.1437-0.00220.1795-6.36291.0023-2.2044
262.0247-0.1966-3.25026.29181.5715.52750.54820.00690.2786-0.1129-0.26940.1621-0.9337-0.218-0.27880.8711-0.02990.11550.5919-0.14540.678813.641745.5029-5.1885
277.3689-2.2746-0.04251.7742.14157.60260.2499-0.40360.19180.2462-0.0737-0.0708-0.05780.0972-0.17630.357-0.13010.06130.1504-0.05310.205319.431740.0686-6.9733
280.87450.0507-0.73920.14230.4512.58920.10690.0810.3076-0.0772-0.0090.09-0.5934-0.106-0.09790.3430.0152-0.00310.050.06450.282820.621738.6767-27.7868
291.7480.51320.04762.16780.00180.6228-0.04730.19080.0387-0.12050.04420.0217-0.13240.05870.00310.1157-0.0456-0.0110.0870.05220.045432.098719.6088-39.9853
300.2879-0.30240.19620.64570.27561.2324-0.03510.07570.1343-0.02370.0571-0.1875-0.18170.1093-0.0220.2017-0.0858-0.00310.15010.03350.200138.219720.6061-25.7061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 18
2X-RAY DIFFRACTION2A19 - 86
3X-RAY DIFFRACTION3A87 - 183
4X-RAY DIFFRACTION4A184 - 306
5X-RAY DIFFRACTION5A307 - 427
6X-RAY DIFFRACTION6B2 - 21
7X-RAY DIFFRACTION7B22 - 127
8X-RAY DIFFRACTION8B128 - 145
9X-RAY DIFFRACTION9B146 - 306
10X-RAY DIFFRACTION10B307 - 427
11X-RAY DIFFRACTION11C2 - 22
12X-RAY DIFFRACTION12C23 - 144
13X-RAY DIFFRACTION13C145 - 154
14X-RAY DIFFRACTION14C155 - 306
15X-RAY DIFFRACTION15C307 - 427
16X-RAY DIFFRACTION16D1 - 31
17X-RAY DIFFRACTION17D32 - 144
18X-RAY DIFFRACTION18D145 - 154
19X-RAY DIFFRACTION19D155 - 306
20X-RAY DIFFRACTION20D307 - 427
21X-RAY DIFFRACTION21E-1 - 20
22X-RAY DIFFRACTION22E21 - 50
23X-RAY DIFFRACTION23E51 - 174
24X-RAY DIFFRACTION24E175 - 306
25X-RAY DIFFRACTION25E307 - 427
26X-RAY DIFFRACTION26F1 - 20
27X-RAY DIFFRACTION27F21 - 51
28X-RAY DIFFRACTION28F52 - 144
29X-RAY DIFFRACTION29F145 - 306
30X-RAY DIFFRACTION30F307 - 427

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