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- PDB-9j9n: artificial mononuclear Zn-bound metalloprotein 2 (M2:Zn) -

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Basic information

Entry
Database: PDB / ID: 9j9n
Titleartificial mononuclear Zn-bound metalloprotein 2 (M2:Zn)
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: 2.86 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)74,2754
Polymers74,1442
Non-polymers1312
Water18010
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)111,4136
Polymers111,2163
Non-polymers1963
Water543
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 area7040 Å2
ΔGint-174 kcal/mol
Surface area39860 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)111,4136
Polymers111,2163
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7010 Å2
ΔGint-165 kcal/mol
Surface area39990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.120, 136.120, 48.880
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: 37072.109 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.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 3.53 Å3/Da / Density % sol: 65.12 %
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: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.86→30 Å / Num. obs: 23436 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC1/2: 0.985 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.127 / Net I/σ(I): 4.24
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.86-3.030.53826120.5730.7611
3.03-3.240.31323760.8460.4421
3.24-3.490.17321430.9350.2441
3.49-3.820.14318240.9470.2011
3.82-4.260.08816850.9760.1241
4.26-4.90.07615020.980.1071
4.9-5.960.07411880.9750.1031
5.96-8.270.0698520.9770.0961
8.27-300.0534730.9860.0751

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→29.47 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 15.447 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 0.885 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24989 1172 5 %RANDOM
Rwork0.19376 ---
obs0.19662 22259 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.665 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0.41 Å20 Å2
2---0.82 Å2-0 Å2
3---2.67 Å2
Refinement stepCycle: 1 / Resolution: 2.86→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 2 10 5052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0115150
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164468
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.7816986
X-RAY DIFFRACTIONr_angle_other_deg0.4621.74210181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.935656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.862520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90310706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0570.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026418
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021358
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_it4.5586.4782642
X-RAY DIFFRACTIONr_mcbond_other4.5536.4772642
X-RAY DIFFRACTIONr_mcangle_it6.90511.6293292
X-RAY DIFFRACTIONr_mcangle_other6.90711.6293293
X-RAY DIFFRACTIONr_scbond_it5.246.8952508
X-RAY DIFFRACTIONr_scbond_other5.2396.8952509
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.30412.4713695
X-RAY DIFFRACTIONr_long_range_B_refined11.95879.221255
X-RAY DIFFRACTIONr_long_range_B_other11.95879.221256
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.86→2.931 Å
RfactorNum. reflection% reflection
Rfree0.353 84 -
Rwork0.303 1602 -
obs--98.65 %

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