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- PDB-6ixx: Crystal structure of a complex between psychrophilic marine prote... -

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Basic information

Entry
Database: PDB / ID: 6ixx
TitleCrystal structure of a complex between psychrophilic marine protease MP and its inhibitor LupI
Components
  • Alkaline metalloprotease
  • LupI
KeywordsHYDROLASE/INIHBITOR / psychrophilic marine protease / protein-protein complex / HYDROLASE-INIHBITOR complex
Function / homology
Function and homology information


metalloendopeptidase inhibitor activity / extracellular matrix / metalloendopeptidase activity / periplasmic space / calcium ion binding / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Protease inhibitor / Alkaline proteinase inhibitor/ Outer membrane lipoprotein Omp19 / Protease inhibitor Inh / Protease inhibitor, beta-barrel domain / Metallo-peptidase family M12B Reprolysin-like / Peptidase M10 serralysin, C-terminal / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal ...Protease inhibitor / Alkaline proteinase inhibitor/ Outer membrane lipoprotein Omp19 / Protease inhibitor Inh / Protease inhibitor, beta-barrel domain / Metallo-peptidase family M12B Reprolysin-like / Peptidase M10 serralysin, C-terminal / Peptidase M10B / Serralysin-like metallopeptidase domain / Peptidase M10 serralysin C terminal / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Alkaline metalloprotease / LupI
Similarity search - Component
Biological speciesFlavobacterium sp. YS-80-122 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsHao, J.H. / Zhang, L.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China41376175 China
CitationJournal: To be published
Title: Crystal structure of a complex between psychrophilic marine protease MP and its inhibitor LupI
Authors: Hao, J.H.
History
DepositionDec 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkaline metalloprotease
I: LupI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,56711
Polymers59,1812
Non-polymers3869
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-85 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.664, 51.852, 102.142
Angle α, β, γ (deg.)90.000, 97.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alkaline metalloprotease


Mass: 48632.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium sp. YS-80-122 (bacteria) / Plasmid details: yellow sea in china / References: UniProt: D0VMS8
#2: Protein LupI


Mass: 10548.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium sp. YS-80-122 (bacteria) / Plasmid details: yellow sea in china / References: UniProt: G3MEU6
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthor states that the sequence G3MEU6 may have errors in sequencing, and this time the sequence is ...Author states that the sequence G3MEU6 may have errors in sequencing, and this time the sequence is re-sequence verified to be Leu.

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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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5 / Details: 0.2M NaCl 0.1M MES 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. obs: 35471 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 17.813
Reflection shellResolution: 1.999→2.07 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.342 / Num. unique obs: 35471 / Rsym value: 0.342 / % possible all: 85.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U1R

3u1r


Resolution: 1.999→38.672 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.03
RfactorNum. reflection% reflection
Rfree0.23 1760 5.09 %
Rwork0.184 --
obs0.1862 34563 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.76 Å2 / Biso mean: 28.5577 Å2 / Biso min: 14.73 Å2
Refinement stepCycle: final / Resolution: 1.999→38.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4175 0 9 244 4428
Biso mean--24.38 26.52 -
Num. residues----560
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9991-2.05320.2551000.20291771187167
2.0532-2.11360.28211410.21632255239686
2.1136-2.18180.28491460.21092516266295
2.1818-2.25980.26131170.21582566268396
2.2598-2.35030.24161430.212611275498
2.3503-2.45720.24481540.20582599275398
2.4572-2.58670.25351200.20022615273598
2.5867-2.74880.24381480.21152576272497
2.7488-2.96090.27621550.206326312786100
2.9609-3.25880.24391300.20512666279699
3.2588-3.730.22351320.18082650278298
3.73-4.69810.19431360.14422639277598
4.6981-38.67960.17011380.14522708284698
Refinement TLS params.Method: refined / Origin x: 16.5939 Å / Origin y: 14.2576 Å / Origin z: 24.6993 Å
111213212223313233
T0.249 Å20.0548 Å2-0.0273 Å2-0.2267 Å2-0.0101 Å2--0.1854 Å2
L0.1979 °20.2014 °2-0.0605 °2-1.5198 °2-0.0683 °2--0.2499 °2
S0.0035 Å °-0.0138 Å °0.0387 Å °-0.4893 Å °-0.0563 Å °0.0903 Å °0.0052 Å °0.0091 Å °0.0372 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA18 - 480
2X-RAY DIFFRACTION1allI2 - 98
3X-RAY DIFFRACTION1allB1 - 257
4X-RAY DIFFRACTION1allD1 - 8
5X-RAY DIFFRACTION1allC1

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