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- PDB-8j9d: Crystal structure of M61 peptidase (bestatin-bound) from Xanthomo... -

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Basic information

Entry
Database: PDB / ID: 8j9d
TitleCrystal structure of M61 peptidase (bestatin-bound) from Xanthomonas campestris
ComponentsPutative glycyl aminopeptidase
KeywordsHYDROLASE / M61 peptidase / glycyl aminopeptidase / apo-form
Function / homology
Function and homology information


aminopeptidase activity
Similarity search - Function
Peptidase M61, catalytic domain / Peptidase M61 / Peptidase M61, N-terminal domain / M61 glycyl aminopeptidase / Peptidase M61 N-terminal domain / Tetratricopeptide TPR-3 / Tetratricopeptide repeat / Peptidase M4/M1, CTD superfamily / PDZ domain profile. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Chem-BES / Glycyl aminopeptidase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris B100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYadav, P. / Kumar, A. / Kulkarni, B.S. / Jamdar, S.N. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
CitationJournal: Febs J. / Year: 2024
Title: Crystal structure of a newly identified M61 family aminopeptidase with broad substrate specificity that is solely responsible for recycling acidic amino acids.
Authors: Jamdar, S.N. / Yadav, P. / Kulkarni, B.S. / Kumar, A. / Makde, R.D.
History
DepositionMay 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative glycyl aminopeptidase
B: Putative glycyl aminopeptidase
C: Putative glycyl aminopeptidase
D: Putative glycyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,66815
Polymers287,8374
Non-polymers1,83211
Water39,1292172
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.008, 95.196, 144.489
Angle α, β, γ (deg.)90.000, 104.472, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASPASP(chain 'A' and (resid 22 through 92 or resid 94...AA22 - 9143 - 112
12VALVALGLNGLN(chain 'A' and (resid 22 through 92 or resid 94...AA94 - 128115 - 149
13SERSERLYSLYS(chain 'A' and (resid 22 through 92 or resid 94...AA131 - 162152 - 183
14ALAALAMETMET(chain 'A' and (resid 22 through 92 or resid 94...AA165 - 179186 - 200
15THRTHRVALVAL(chain 'A' and (resid 22 through 92 or resid 94...AA181 - 464202 - 485
16THRTHRLEULEU(chain 'A' and (resid 22 through 92 or resid 94...AA466 - 479487 - 500
17SERSERASPASP(chain 'A' and (resid 22 through 92 or resid 94...AA481 - 617502 - 638
18LEULEUARGARG(chain 'A' and (resid 22 through 92 or resid 94...AA619 - 626640 - 647
19ZNZNZNZN(chain 'A' and (resid 22 through 92 or resid 94...AE701
21ALAALAASPASP(chain 'B' and (resid 22 through 92 or resid 94...BB22 - 9143 - 112
22VALVALGLNGLN(chain 'B' and (resid 22 through 92 or resid 94...BB94 - 128115 - 149
23SERSERLYSLYS(chain 'B' and (resid 22 through 92 or resid 94...BB131 - 162152 - 183
24ALAALAMETMET(chain 'B' and (resid 22 through 92 or resid 94...BB165 - 179186 - 200
25THRTHRVALVAL(chain 'B' and (resid 22 through 92 or resid 94...BB181 - 464202 - 485
26THRTHRLEULEU(chain 'B' and (resid 22 through 92 or resid 94...BB466 - 479487 - 500
27SERSERASPASP(chain 'B' and (resid 22 through 92 or resid 94...BB481 - 617502 - 638
28LEULEUARGARG(chain 'B' and (resid 22 through 92 or resid 94...BB619 - 626640 - 647
29ZNZNZNZN(chain 'B' and (resid 22 through 92 or resid 94...BG701
31ALAALAASPASP(chain 'C' and (resid 22 through 92 or resid 94...CC22 - 9143 - 112
32VALVALGLNGLN(chain 'C' and (resid 22 through 92 or resid 94...CC94 - 128115 - 149
33SERSERLYSLYS(chain 'C' and (resid 22 through 92 or resid 94...CC131 - 162152 - 183
34ALAALAMETMET(chain 'C' and (resid 22 through 92 or resid 94...CC165 - 179186 - 200
35THRTHRVALVAL(chain 'C' and (resid 22 through 92 or resid 94...CC181 - 464202 - 485
36THRTHRLEULEU(chain 'C' and (resid 22 through 92 or resid 94...CC466 - 479487 - 500
37SERSERASPASP(chain 'C' and (resid 22 through 92 or resid 94...CC481 - 617502 - 638
38LEULEUARGARG(chain 'C' and (resid 22 through 92 or resid 94...CC619 - 626640 - 647
39ZNZNZNZN(chain 'C' and (resid 22 through 92 or resid 94...CJ701
41ALAALAASPASP(chain 'D' and (resid 22 through 92 or resid 94...DD22 - 9143 - 112
42VALVALGLNGLN(chain 'D' and (resid 22 through 92 or resid 94...DD94 - 128115 - 149
43SERSERLYSLYS(chain 'D' and (resid 22 through 92 or resid 94...DD131 - 162152 - 183
44ALAALAMETMET(chain 'D' and (resid 22 through 92 or resid 94...DD165 - 179186 - 200
45THRTHRVALVAL(chain 'D' and (resid 22 through 92 or resid 94...DD181 - 464202 - 485
46THRTHRLEULEU(chain 'D' and (resid 22 through 92 or resid 94...DD466 - 479487 - 500
47SERSERASPASP(chain 'D' and (resid 22 through 92 or resid 94...DD481 - 617502 - 638
48LEULEUARGARG(chain 'D' and (resid 22 through 92 or resid 94...DD619 - 626640 - 647
49ZNZNZNZN(chain 'D' and (resid 22 through 92 or resid 94...DM701

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative glycyl aminopeptidase


Mass: 71959.133 Da / Num. of mol.: 4 / Mutation: Q22A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris B100 (bacteria)
Gene: XCCB100_3176 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: B0RY21

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Non-polymers , 5 types, 2183 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BES / 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID / BESTATIN / Ubenimex


Mass: 308.373 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H24N2O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: protease inhibitor*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2172 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 49.33 %
Crystal growTemperature: 294 K / Method: batch mode / pH: 8.5
Details: 0.1M Tris-Cl pH 8.5, 0.1M NaCl, 6-11% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 2, 2017 / Details: Mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.9→47.6 Å / Num. obs: 215479 / % possible obs: 99.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 20.57 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.045 / Rrim(I) all: 0.08 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 9862 / CC1/2: 0.828 / Rpim(I) all: 0.293 / Rrim(I) all: 0.495 / % possible all: 92.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RESOLVEmodel building
Cootmodel building
PHENIX1.14_3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.36 Å / SU ML: 0.178 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4505 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1909 10802 5.02 %
Rwork0.1712 204549 -
obs0.1722 215351 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.56 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19064 0 114 2182 21360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004119761
X-RAY DIFFRACTIONf_angle_d0.726626838
X-RAY DIFFRACTIONf_chiral_restr0.04852838
X-RAY DIFFRACTIONf_plane_restr0.00523497
X-RAY DIFFRACTIONf_dihedral_angle_d13.295211655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.29323270.27236040X-RAY DIFFRACTION88.79
1.92-1.940.26263480.23956908X-RAY DIFFRACTION99.81
1.94-1.970.25713840.22916766X-RAY DIFFRACTION99.85
1.97-1.990.25063390.21826821X-RAY DIFFRACTION99.89
1.99-2.020.2223360.21216848X-RAY DIFFRACTION99.86
2.02-2.050.21983590.20946795X-RAY DIFFRACTION99.78
2.05-2.080.26383700.20996854X-RAY DIFFRACTION99.88
2.08-2.110.21433670.2016813X-RAY DIFFRACTION99.81
2.11-2.140.22373850.20026806X-RAY DIFFRACTION99.9
2.14-2.170.23063650.19256830X-RAY DIFFRACTION99.78
2.17-2.210.2363300.19586836X-RAY DIFFRACTION99.92
2.21-2.250.21163660.18346844X-RAY DIFFRACTION99.78
2.25-2.30.22573570.1856801X-RAY DIFFRACTION99.78
2.3-2.340.20863640.18166832X-RAY DIFFRACTION99.85
2.34-2.390.22223570.18716846X-RAY DIFFRACTION99.82
2.39-2.450.20113690.18376855X-RAY DIFFRACTION99.81
2.45-2.510.20313560.18486786X-RAY DIFFRACTION99.79
2.51-2.580.21323440.18016889X-RAY DIFFRACTION99.75
2.58-2.650.2043670.17846795X-RAY DIFFRACTION99.82
2.65-2.740.19753730.18126839X-RAY DIFFRACTION99.85
2.74-2.840.19793730.17836856X-RAY DIFFRACTION99.79
2.84-2.950.20174010.17726789X-RAY DIFFRACTION99.81
2.95-3.090.19833750.17816837X-RAY DIFFRACTION99.64
3.09-3.250.19143340.17586864X-RAY DIFFRACTION99.78
3.25-3.450.17813840.16596854X-RAY DIFFRACTION99.75
3.45-3.720.17353370.15996898X-RAY DIFFRACTION99.79
3.72-4.090.17013450.15176889X-RAY DIFFRACTION99.89
4.09-4.680.13273710.12456905X-RAY DIFFRACTION99.81
4.68-5.90.13053510.12566950X-RAY DIFFRACTION99.69
5.9-44.360.15453680.13586903X-RAY DIFFRACTION97.79
Refinement TLS params.Method: refined / Origin x: 96.8207137826 Å / Origin y: -5.14292010583 Å / Origin z: 35.0859423663 Å
111213212223313233
T0.169736089653 Å20.00691494839594 Å20.0220758728413 Å2-0.151571506652 Å2-0.00935882690394 Å2--0.137580842597 Å2
L0.264091537762 °20.0451276182816 °20.123186756114 °2-0.0143188274031 °2-0.000212916346308 °2--0.141090647153 °2
S-0.00238601531144 Å °0.0185674893942 Å °-0.00176087547366 Å °-0.00855910644401 Å °-0.00277026085282 Å °0.00579972742802 Å °0.00188175315195 Å °0.01603947953 Å °0.00543655659983 Å °
Refinement TLS groupSelection details: all

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