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- PDB-7xrx: insulin-cleaving membrane protease-ICMP -

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Basic information

Entry
Database: PDB / ID: 7xrx
Titleinsulin-cleaving membrane protease-ICMP
ComponentsInsulin-cleaving metalloproteinase outer membrane protein
KeywordsMETAL BINDING PROTEIN / Pseudomonas aeruginosa / metallopeptidase
Function / homology
Function and homology information


M75 peptidase, HXXE motif / Imelysin-like domain / Imelysin-like domain superfamily / Imelysin / A middle domain of Talin 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Insulin-cleaving metalloproteinase outer membrane protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.882 Å
AuthorsWang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted ICMP from P. aeruginosa
Authors: Wang, J.
History
DepositionMay 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin-cleaving metalloproteinase outer membrane protein
B: Insulin-cleaving metalloproteinase outer membrane protein
C: Insulin-cleaving metalloproteinase outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1176
Polymers128,9973
Non-polymers1203
Water26,7881487
1
A: Insulin-cleaving metalloproteinase outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0392
Polymers42,9991
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area16220 Å2
MethodPISA
2
B: Insulin-cleaving metalloproteinase outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0392
Polymers42,9991
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area16080 Å2
MethodPISA
3
C: Insulin-cleaving metalloproteinase outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0392
Polymers42,9991
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.927, 78.141, 99.916
Angle α, β, γ (deg.)90.000, 113.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Insulin-cleaving metalloproteinase outer membrane protein


Mass: 42998.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: icmP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HW32
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1487 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 1.6 M sodium citrate tri-basic dihydrate at pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.882→34.372 Å / Num. obs: 97961 / % possible obs: 99.4 % / Redundancy: 5.8 % / CC1/2: 0.839 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 54651 / CC1/2: 0.839

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.882→34.372 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 4565 4.66 %
Rwork0.1459 93396 -
obs0.1479 97961 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.42 Å2 / Biso mean: 23.046 Å2 / Biso min: 2.26 Å2
Refinement stepCycle: final / Resolution: 1.882→34.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9015 0 3 1487 10505
Biso mean--20.88 34.03 -
Num. residues----1193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079171
X-RAY DIFFRACTIONf_angle_d0.83712415
X-RAY DIFFRACTIONf_chiral_restr0.0441364
X-RAY DIFFRACTIONf_plane_restr0.0041661
X-RAY DIFFRACTIONf_dihedral_angle_d14.5295495
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8821-1.90350.2202610.2014141544
1.9035-1.92590.26491370.1966309297
1.9259-1.94930.27751520.1897313898
1.9493-1.9740.24561430.1744308498
1.974-20.23181370.166316098
2-2.02740.22841520.1582312499
2.0274-2.05630.1921570.1566311598
2.0563-2.0870.20081520.1476313399
2.087-2.11960.19331560.1474317599
2.1196-2.15440.19011580.1394315399
2.1544-2.19150.21261470.145317599
2.1915-2.23140.18391460.1431315199
2.2314-2.27430.19111580.1432314999
2.2743-2.32070.1791430.1418320499
2.3207-2.37110.20321610.1455315999
2.3711-2.42630.19161680.1456313399
2.4263-2.4870.21071550.1461318399
2.487-2.55420.21851730.1467315699
2.5542-2.62930.18461440.1478318599
2.6293-2.71410.17361260.15383210100
2.7141-2.81110.19221400.1532319199
2.8111-2.92360.19141440.15053209100
2.9236-3.05660.191680.14963162100
3.0566-3.21760.19751600.153219100
3.2176-3.4190.18331780.13983192100
3.419-3.68270.15281880.13243174100
3.6827-4.05280.15381510.12713225100
4.0528-4.63810.15891450.12563248100
4.6381-5.83880.1811960.14883202100
5.8388-34.3720.17551690.15253280100

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