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- PDB-5zjk: Structure of myroilysin -

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Basic information

Entry
Database: PDB / ID: 5zjk
TitleStructure of myroilysin
ComponentsMyroilysin
KeywordsHYDROLASE
Function / homology
Function and homology information


metalloendopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Peptidase M12A / Astacin (Peptidase family M12A) / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
PHOSPHATE ION / Myroilysin
Similarity search - Component
Biological speciesMyroides sp. CSLB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsLi, W.D. / Ran, T.T. / Xu, D.Q. / Wang, W.W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770074 China
National Natural Science Foundation of China31770050 China
Citation
Journal: Int.J.Biol.Macromol. / Year: 2019
Title: Crystal structure of mature myroilysin and implication for its activation mechanism.
Authors: Ran, T. / Li, W. / Sun, B. / Xu, M. / Qiu, S. / Xu, D.Q. / He, J. / Wang, W.
#1: Journal: To Be Published
Title: Structural insight into the activation of myroilysin
Authors: Li, W.D. / Ran, T.T. / Xu, D.Q. / Wang, W.W.
History
DepositionMar 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myroilysin
B: Myroilysin
C: Myroilysin
D: Myroilysin
E: Myroilysin
F: Myroilysin
G: Myroilysin
H: Myroilysin
I: Myroilysin
J: Myroilysin
K: Myroilysin
L: Myroilysin
M: Myroilysin
N: Myroilysin
O: Myroilysin
P: Myroilysin
Q: Myroilysin
R: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)435,81748
Polymers433,50018
Non-polymers2,31730
Water13,457747
1
A: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1492
Polymers24,0831
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2443
Polymers24,0831
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1492
Polymers24,0831
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2443
Polymers24,0831
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2443
Polymers24,0831
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2443
Polymers24,0831
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2443
Polymers24,0831
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2443
Polymers24,0831
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2443
Polymers24,0831
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2443
Polymers24,0831
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2443
Polymers24,0831
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1492
Polymers24,0831
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2443
Polymers24,0831
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1492
Polymers24,0831
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1492
Polymers24,0831
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2443
Polymers24,0831
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
Q: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2443
Polymers24,0831
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
R: Myroilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1492
Polymers24,0831
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.176, 115.902, 163.354
Angle α, β, γ (deg.)90.00, 93.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Myroilysin


Mass: 24083.340 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myroides sp. CSLB8 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0DZ84
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 747 / 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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 142484 / % possible obs: 99.5 % / Redundancy: 7 % / Rpim(I) all: 0.071 / Net I/σ(I): 9.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 20724 / Rpim(I) all: 0.317 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.6→19.993 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.72
RfactorNum. reflection% reflection
Rfree0.2537 7188 5.05 %
Rwork0.1866 --
obs0.19 142443 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29247 0 78 747 30072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00330255
X-RAY DIFFRACTIONf_angle_d0.69341223
X-RAY DIFFRACTIONf_dihedral_angle_d13.09410317
X-RAY DIFFRACTIONf_chiral_restr0.0284389
X-RAY DIFFRACTIONf_plane_restr0.0035274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.62950.35762370.28694524X-RAY DIFFRACTION99
2.6295-2.66030.33932460.27044451X-RAY DIFFRACTION99
2.6603-2.69270.31512460.2674426X-RAY DIFFRACTION99
2.6927-2.72670.32272320.26244499X-RAY DIFFRACTION100
2.7267-2.76250.3112380.25534489X-RAY DIFFRACTION100
2.7625-2.80030.32782280.25354483X-RAY DIFFRACTION99
2.8003-2.84010.3082520.25394509X-RAY DIFFRACTION100
2.8401-2.88240.34882380.25074459X-RAY DIFFRACTION100
2.8824-2.92730.32542460.24614470X-RAY DIFFRACTION100
2.9273-2.97520.3142370.23754486X-RAY DIFFRACTION99
2.9752-3.02630.31382580.23464465X-RAY DIFFRACTION99
3.0263-3.08110.27322500.23194486X-RAY DIFFRACTION99
3.0811-3.14020.30442190.22554495X-RAY DIFFRACTION99
3.1402-3.2040.29732480.23394472X-RAY DIFFRACTION99
3.204-3.27340.30982340.22154510X-RAY DIFFRACTION100
3.2734-3.34920.29362330.20994491X-RAY DIFFRACTION100
3.3492-3.43260.28132470.20554473X-RAY DIFFRACTION100
3.4326-3.52490.26062420.19154502X-RAY DIFFRACTION100
3.5249-3.6280.23872250.1794547X-RAY DIFFRACTION100
3.628-3.74440.23292270.17314501X-RAY DIFFRACTION100
3.7444-3.87730.22952440.16564536X-RAY DIFFRACTION100
3.8773-4.03130.24182650.16054496X-RAY DIFFRACTION100
4.0313-4.21310.20772440.14454486X-RAY DIFFRACTION100
4.2131-4.4330.20142440.13884578X-RAY DIFFRACTION100
4.433-4.70730.20152450.1414507X-RAY DIFFRACTION100
4.7073-5.06530.19312440.14084540X-RAY DIFFRACTION100
5.0653-5.56510.22252280.14764562X-RAY DIFFRACTION100
5.5651-6.34770.2262300.16774567X-RAY DIFFRACTION100
6.3477-7.9140.22432650.14914556X-RAY DIFFRACTION100
7.914-100.19081960.13724689X-RAY DIFFRACTION99

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