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- PDB-2fgr: High resolution Xray structure of Omp32 -

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Basic information

Entry
Database: PDB / ID: 2fgr
TitleHigh resolution Xray structure of Omp32
Components
  • Outer membrane porin protein 32
  • PAP
KeywordsMEMBRANE PROTEIN / Omp32 Porin Outer membrane protein
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Porin, Neisseria sp. type / Gram-negative porin / Porin domain, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane porin protein 32
Similarity search - Component
Biological speciesDelftia acidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZeth, K. / Zachariae, U. / Engelhardt, H.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin omp32
Authors: Zachariae, U. / Kluhspies, T. / De, S. / Engelhardt, H. / Zeth, K.
History
DepositionDec 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999The first residue is a pyroglutamate which might appear as GLN in Swissprot but we have it in the ...The first residue is a pyroglutamate which might appear as GLN in Swissprot but we have it in the opened form as Glu in the structure.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane porin protein 32
B: PAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0827
Polymers35,7692
Non-polymers3125
Water7,350408
1
A: Outer membrane porin protein 32
B: PAP
hetero molecules

A: Outer membrane porin protein 32
B: PAP
hetero molecules

A: Outer membrane porin protein 32
B: PAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,24621
Polymers107,3086
Non-polymers93715
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)106.410, 106.410, 93.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-502-

CA

21A-893-

HOH

31B-311-

HOH

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Components

#1: Protein Outer membrane porin protein 32 / OMP32


Mass: 34848.602 Da / Num. of mol.: 1 / Mutation: Q1E / Source method: isolated from a natural source / Source: (natural) Delftia acidovorans (bacteria) / References: UniProt: P24305
#2: Protein/peptide PAP


Mass: 920.881 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 4.28 Å3/Da / Density % sol: 71.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0053 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0053 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 92517 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 1.5→1.59 Å / % possible all: 78.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT1.701data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.021 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 4618 5 %RANDOM
Rwork0.15 ---
all0.151 96291 --
obs0.151 92517 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.29 Å20 Å2
2--0.59 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2527 0 13 408 2948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0212580
X-RAY DIFFRACTIONr_bond_other_d0.0030.022257
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.953481
X-RAY DIFFRACTIONr_angle_other_deg0.92635237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4875338
X-RAY DIFFRACTIONr_chiral_restr0.1420.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023000
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02559
X-RAY DIFFRACTIONr_nbd_refined0.270.2442
X-RAY DIFFRACTIONr_nbd_other0.2850.22766
X-RAY DIFFRACTIONr_nbtor_other0.0880.21715
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2279
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.223
X-RAY DIFFRACTIONr_mcbond_it1.6651.51650
X-RAY DIFFRACTIONr_mcangle_it2.61222587
X-RAY DIFFRACTIONr_scbond_it4.253930
X-RAY DIFFRACTIONr_scangle_it6.2164.5894
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.33 265
Rwork0.292 5208
obs-5473

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