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- PDB-6hc6: The structure of BSAP, a zinc aminopeptidase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 6hc6
TitleThe structure of BSAP, a zinc aminopeptidase from Bacillus subtilis
ComponentsAminopeptidase YwaD
KeywordsMETAL BINDING PROTEIN / aminopeptidase / zinc binding protein / geobacillus stearothermophilus / PA-domain
Function / homology
Function and homology information


aminopeptidase B / bacterial leucyl aminopeptidase / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Peptidase M28 family / PA domain superfamily / PA domain / PA domain / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
ACETATE ION / Aminopeptidase YwaD
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsRogoulenko, E. / Lansky, S. / Faygenboim, R. / Cohen, T. / Alhadeff, R. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: To be published
Authors: Alhadeff, R. / Faygenboim, R. / Lansky, S. / Rogoulenko, E. / Cohen, T. / Fundoiano-Hershcovitz, Y. / Feinberg, H. / Shoham, Y. / Shoham, G.
History
DepositionAug 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase YwaD
B: Aminopeptidase YwaD
C: Aminopeptidase YwaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,17326
Polymers148,5453
Non-polymers1,62823
Water18,8621047
1
A: Aminopeptidase YwaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8827
Polymers49,5151
Non-polymers3676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminopeptidase YwaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9487
Polymers49,5151
Non-polymers4336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Aminopeptidase YwaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,34312
Polymers49,5151
Non-polymers82711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)224.922, 224.922, 42.502
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Aminopeptidase YwaD / Arginyl aminopeptidase / BSAP / Leucyl aminopeptidase


Mass: 49515.082 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: ywaD, BSU38470, ipa-8r / Production host: Escherichia coli (E. coli)
References: UniProt: P25152, aminopeptidase B, bacterial leucyl aminopeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1047 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 2K MME, 0.1M LiSO4, 4mM MnCl2, 0.1M acetate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.77→48.7 Å / Num. obs: 120817 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.9
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.1089 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CP7
Resolution: 1.77→48.697 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.98
RfactorNum. reflection% reflection
Rfree0.2027 2902 2.4 %
Rwork0.1647 --
obs0.1656 120790 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.77→48.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9384 0 88 1047 10519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069702
X-RAY DIFFRACTIONf_angle_d0.82313107
X-RAY DIFFRACTIONf_dihedral_angle_d3.4638158
X-RAY DIFFRACTIONf_chiral_restr0.0531462
X-RAY DIFFRACTIONf_plane_restr0.0051705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.7990.44191590.36435476X-RAY DIFFRACTION100
1.799-1.83010.2579980.24575618X-RAY DIFFRACTION100
1.8301-1.86330.27491270.20785583X-RAY DIFFRACTION100
1.8633-1.89920.21531610.19065512X-RAY DIFFRACTION100
1.8992-1.93790.22041370.19155627X-RAY DIFFRACTION100
1.9379-1.98010.22941560.19055470X-RAY DIFFRACTION100
1.9801-2.02620.22021430.19125653X-RAY DIFFRACTION100
2.0262-2.07680.19921650.18455498X-RAY DIFFRACTION100
2.0768-2.1330.21171110.17295647X-RAY DIFFRACTION100
2.133-2.19570.20711260.16935568X-RAY DIFFRACTION100
2.1957-2.26660.23871600.16875592X-RAY DIFFRACTION100
2.2666-2.34760.21451430.17395603X-RAY DIFFRACTION100
2.3476-2.44160.22821230.17165569X-RAY DIFFRACTION100
2.4416-2.55270.19881540.16655590X-RAY DIFFRACTION100
2.5527-2.68730.21931400.16875649X-RAY DIFFRACTION100
2.6873-2.85570.22481070.17445643X-RAY DIFFRACTION100
2.8557-3.07610.20121270.17025646X-RAY DIFFRACTION100
3.0761-3.38560.18981580.16245617X-RAY DIFFRACTION100
3.3856-3.87530.17851300.14245743X-RAY DIFFRACTION100
3.8753-4.88180.16551370.12545691X-RAY DIFFRACTION100
4.8818-48.71550.17661400.1525893X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.1051-1.6334-0.09464.11910.98813.0931-0.0085-0.1482-0.53330.3280.00220.00830.2138-0.02160.0250.1448-0.0173-0.04120.17250.03890.2181-81.5937404.917851.1234
24.3247-1.9137-0.16182.1547-0.15350.52750.04520.08330.31560.1460.08990.1429-0.0878-0.0028-0.140.177-0.00670.03260.20380.01230.2373-98.5576431.031452.4671
32.7719-0.1863-0.35591.74290.09451.4820.06370.5376-0.0078-0.07640.002-0.22250.03790.0975-0.03830.1160.0214-0.01890.2803-0.02490.1485-76.2446415.392340.8973
41.1935-0.20050.0891.3379-0.00821.3784-0.016-0.30560.11340.16740.09750.1483-0.1223-0.2779-0.06060.15160.01050.0360.2365-0.00880.1369-54.3061384.627456.936
51.7971-0.02950.03560.6118-0.270.2574-0.03470.02290.01410.01030.327-0.7715-0.11990.3275-0.19650.2533-0.02570.00970.3552-0.27470.7306-23.1941391.922853.5795
61.62290.3061-0.29722.1086-0.07381.18540.1118-0.4816-0.07780.2060.0213-0.04070.1104-0.1299-0.05270.1319-0.0072-0.01720.1891-0.00150.1077-47.3001376.995458.3121
71.71050.10040.50041.5925-0.16851.35610.04310.0355-0.177-0.16360.09470.14710.1438-0.1253-0.10920.1369-0.0423-0.02480.15450.00550.1114-52.3686374.841444.7967
81.48320.61540.45461.3544-0.97892.1618-0.04280.25180.1449-0.53330.0536-0.0772-0.1430.060.010.2023-0.0202-0.0040.17970.00130.1174-47.6417388.108639.8954
93.76650.60410.29422.5796-0.08381.99770.0309-0.0169-0.2756-0.22560.17080.00930.1024-0.1567-0.15420.1539-0.0343-0.00560.1614-0.01850.0801-53.0824376.645841.3738
101.36250.3591-0.57011.5166-0.34961.60560.0933-0.17170.14580.1807-0.0416-0.1512-0.11730.2095-0.03850.1595-0.0468-0.02270.2717-0.06050.1481-85.6838378.01247.3875
111.4819-0.5531-0.081.2165-0.33341.4310.2559-0.2613-0.63990.64160.0787-0.66390.36240.2596-0.21460.4004-0.0259-0.27470.3497-0.02160.5395-94.2849358.116156.3547
120.7317-0.15760.28890.66470.43660.50310.42610.1201-0.59660.32940.1969-0.77060.5530.37890.1660.33930.2134-0.48070.1513-0.02381.0468-97.639342.802345.304
131.67210.15570.22622.289-0.13041.44930.10970.020.09080.0433-0.0040.0871-0.0005-0.0422-0.09060.1223-0.02430.00460.1904-0.02250.0986-98.8996375.728741.3454
141.52-0.37420.00312.3001-0.21081.5770.05770.2191-0.0693-0.28160.01690.07690.13470.0251-0.0750.1607-0.0169-0.01590.2344-0.03540.1034-93.2776372.200834.1361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 234 )
3X-RAY DIFFRACTION3chain 'A' and (resid 235 through 455 )
4X-RAY DIFFRACTION4chain 'B' and (resid 39 through 104 )
5X-RAY DIFFRACTION5chain 'B' and (resid 105 through 211 )
6X-RAY DIFFRACTION6chain 'B' and (resid 212 through 250 )
7X-RAY DIFFRACTION7chain 'B' and (resid 251 through 381 )
8X-RAY DIFFRACTION8chain 'B' and (resid 382 through 411 )
9X-RAY DIFFRACTION9chain 'B' and (resid 412 through 455 )
10X-RAY DIFFRACTION10chain 'C' and (resid 39 through 82 )
11X-RAY DIFFRACTION11chain 'C' and (resid 83 through 124 )
12X-RAY DIFFRACTION12chain 'C' and (resid 125 through 211 )
13X-RAY DIFFRACTION13chain 'C' and (resid 212 through 381 )
14X-RAY DIFFRACTION14chain 'C' and (resid 382 through 455 )

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