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- PDB-9j9o: artificial dinuclear Zn-bound metalloprotein 1 (D1:2Zn) -

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Basic information

Entry
Database: PDB / ID: 9j9o
Titleartificial dinuclear Zn-bound metalloprotein 1 (D1:2Zn)
ComponentsOuter membrane porin F
KeywordsMEMBRANE PROTEIN / artificial metalloprotein
Function / homology
Function and homology information


colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / protein transport / monoatomic ion transmembrane transport / lipid binding / identical protein binding / membrane
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsJeong, W.J. / Song, W.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other private2019R1C1C1003863 Korea, Republic Of
CitationJournal: To Be Published
Title: Metal-Installer: A protein designer tool to create metal-binding sites
Authors: Jeong, W.J. / Song, W.J.
History
DepositionAug 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane porin F
B: Outer membrane porin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2606
Polymers73,9982
Non-polymers2624
Water00
1
A: Outer membrane porin F
hetero molecules

A: Outer membrane porin F
hetero molecules

A: Outer membrane porin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3909
Polymers110,9973
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area9180 Å2
ΔGint-262 kcal/mol
Surface area39920 Å2
MethodPISA
2
B: Outer membrane porin F
hetero molecules

B: Outer membrane porin F
hetero molecules

B: Outer membrane porin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3909
Polymers110,9973
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9190 Å2
ΔGint-274 kcal/mol
Surface area39880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.800, 137.800, 49.545
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Outer membrane porin F / Outer membrane protein 1A / Outer membrane protein B / Outer membrane protein F / Outer membrane ...Outer membrane protein 1A / Outer membrane protein B / Outer membrane protein F / Outer membrane protein IA / Porin OmpF


Mass: 36999.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ompF, cmlB, coa, cry, tolF, b0929, JW0912 / Production host: Escherichia coli (E. coli) / References: UniProt: P02931
#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
Has ligand of interestY
Has protein modificationN

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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: 3.67 Å3/Da / Density % sol: 66.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.3 M MgCl2, 0.1 M MOPS pH 8.0, and 28 % w/v PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Feb 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.99→30 Å / Num. obs: 21105 / % possible obs: 99.4 % / Redundancy: 7.85 % / CC1/2: 0.996 / Rmerge(I) obs: 0.166 / Rrim(I) all: 0.178 / Net I/σ(I): 9.99
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.99-3.170.74214120.7730.9751
3.17-3.390.41214180.9040.5971
3.39-3.660.28713060.8010.3911
3.66-40.19611550.9180.2641
4-4.460.14910190.960.2011
4.46-5.130.0968790.9790.1321
5.13-6.230.0987130.9750.1331
6.23-8.60.0645070.990.0891
8.6-300.032800.9970.0411

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→28.28 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 16.538 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23887 1056 5 %RANDOM
Rwork0.19239 ---
obs0.19471 20048 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 2.99→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5168 0 4 0 5172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0115284
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164574
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.7827168
X-RAY DIFFRACTIONr_angle_other_deg0.4161.74310438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9425678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.769520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2610732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0530.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026608
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021384
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4727.0172718
X-RAY DIFFRACTIONr_mcbond_other5.4727.0172718
X-RAY DIFFRACTIONr_mcangle_it7.80712.6173394
X-RAY DIFFRACTIONr_mcangle_other7.80612.6173395
X-RAY DIFFRACTIONr_scbond_it6.2417.4312566
X-RAY DIFFRACTIONr_scbond_other6.247.432567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.3413.4593775
X-RAY DIFFRACTIONr_long_range_B_refined11.98586.4221859
X-RAY DIFFRACTIONr_long_range_B_other11.98586.4221860
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.994→3.071 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 75 -
Rwork0.294 1412 -
obs--94.71 %

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