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- PDB-7y1s: Crystal structure of apo leucyl aminopeptidase from Bacillus amyl... -

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Basic information

Entry
Database: PDB / ID: 7y1s
TitleCrystal structure of apo leucyl aminopeptidase from Bacillus amyloliquefaciens
Componentsleucyl aminopeptidase
KeywordsHYDROLASE / M17 / leucyl aminopeptidase / leucine aminopeptidase / metallopeptidase
Function / homologyCARBONATE ION / NICKEL (II) ION / :
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.748 Å
AuthorsHuang, P. / Jiang, Z.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of apo leucyl aminopeptidase from Bacillus amyloliquefaciens
Authors: Huang, P. / Jiang, Z.Q.
History
DepositionJun 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Assembly

Deposited unit
A: leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0915
Polymers55,8421
Non-polymers2504
Water75742
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-84 kcal/mol
Surface area21220 Å2
Unit cell
Length a, b, c (Å)200.245, 200.245, 89.022
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-502-

NI

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Components

#1: Protein leucyl aminopeptidase


Mass: 55841.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5C8IUB1, leucyl aminopeptidase
#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
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: 4.78 Å3/Da / Density % sol: 74.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.5 M succinic acid (pH 7.0), 0.1 M Bis-Tris propane (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.748→50 Å / Num. obs: 27747 / % possible obs: 99.24 % / Redundancy: 30.3 % / CC1/2: 0.996 / Net I/σ(I): 21.69
Reflection shellResolution: 2.748→2.848 Å / Num. unique obs: 2734 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JRU

3jru


Resolution: 2.748→37.871 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.601 / SU ML: 0.153 / Cross valid method: FREE R-VALUE / ESU R: 0.275 / ESU R Free: 0.224 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2118 1332 4.814 %
Rwork0.17 26337 -
all0.172 --
obs-27669 99.133 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 58.642 Å2
Baniso -1Baniso -2Baniso -3
1--1.055 Å2-0.527 Å2-0 Å2
2---1.055 Å20 Å2
3---3.422 Å2
Refinement stepCycle: LAST / Resolution: 2.748→37.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 7 42 3763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123783
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.6325104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3385492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23524.22173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.19715655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1481515
X-RAY DIFFRACTIONr_chiral_restr0.1390.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022820
X-RAY DIFFRACTIONr_nbd_refined0.2420.21762
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2127
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2590.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2270.29
X-RAY DIFFRACTIONr_mcbond_it5.5735.6221974
X-RAY DIFFRACTIONr_mcangle_it7.5128.4122464
X-RAY DIFFRACTIONr_scbond_it8.2696.0651806
X-RAY DIFFRACTIONr_scangle_it10.7188.8482639
X-RAY DIFFRACTIONr_lrange_it11.5277.195611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.748-2.8190.355710.2331908X-RAY DIFFRACTION97.5357
2.819-2.8960.336940.2311867X-RAY DIFFRACTION100
2.896-2.980.28940.2131830X-RAY DIFFRACTION100
2.98-3.0720.261890.2091789X-RAY DIFFRACTION99.9468
3.072-3.1720.279770.2011732X-RAY DIFFRACTION100
3.172-3.2840.277890.1891661X-RAY DIFFRACTION100
3.284-3.4080.2341000.1981592X-RAY DIFFRACTION100
3.408-3.5470.281790.1811559X-RAY DIFFRACTION100
3.547-3.7040.182680.1661509X-RAY DIFFRACTION100
3.704-3.8850.208710.1441434X-RAY DIFFRACTION100
3.885-4.0950.15720.1371358X-RAY DIFFRACTION100
4.095-4.3430.17650.1281300X-RAY DIFFRACTION100
4.343-4.6430.161690.1361227X-RAY DIFFRACTION99.9229
4.643-5.0150.248610.1391148X-RAY DIFFRACTION100
5.015-5.4930.176670.1651045X-RAY DIFFRACTION99.8205
5.493-6.1410.248530.209958X-RAY DIFFRACTION100
6.141-7.0890.197460.191863X-RAY DIFFRACTION99.0196
7.089-8.6790.15300.15738X-RAY DIFFRACTION98.3355
8.679-12.2580.171270.142568X-RAY DIFFRACTION94.5946
12.258-37.8710.152100.277251X-RAY DIFFRACTION66.4122

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