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- PDB-6gie: Crystal structure of the Acinetobacter baumannii outer membrane p... -

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Basic information

Entry
Database: PDB / ID: 6gie
TitleCrystal structure of the Acinetobacter baumannii outer membrane protein Omp33
Components33-36 kDa outer membrane protein
KeywordsMEMBRANE PROTEIN / channel
Function / homologyPutative general bacterial porin / Putative general bacterial porin / Putative 34 kDa outer membrane protein / Carbapenem susceptibility porin CarO
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAbellon-Ruiz, J. / Zahn, M. / Basle, A. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Union115525 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Crystal structure of the Acinetobacter baumannii outer membrane protein Omp33.
Authors: Abellon-Ruiz, J. / Zahn, M. / Basle, A. / van den Berg, B.
History
DepositionMay 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 33-36 kDa outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5635
Polymers32,3371
Non-polymers1,2264
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-1 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.680, 73.740, 53.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 33-36 kDa outer membrane protein / Carbapenem susceptibility porin CarO / Putative porin


Mass: 32337.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: carO, ABUW_0187, B4R90_18580, CBI29_03686, CHQ89_12430, CV949_17495, CV951_18190, CV952_18425, CV954_00850
Production host: Escherichia coli (E. coli) / References: UniProt: A0A081GU02, UniProt: A0A062F4L9*PLUS
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 26% PEG 400 0.05M NaCl 0.1M sodium citrate pH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97834 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97834 Å / Relative weight: 1
ReflectionResolution: 2.1→43.1 Å / Num. obs: 16543 / % possible obs: 100 % / Redundancy: 7.1 % / Rpim(I) all: 0.048 / Net I/σ(I): 9.5
Reflection shellResolution: 2.1→2.2 Å / CC1/2: 0.38 / Rpim(I) all: 0.63

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Processing

Software
NameVersionClassification
REFMAC5.8.0216refinement
XDS(1.12_2829: ???)data reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: previous SAD not deposited

Resolution: 2.1→43.1 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.173 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26645 678 5.1 %RANDOM
Rwork0.21332 ---
obs0.216 12743 81.2 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.928 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å20 Å2
2--1.48 Å2-0 Å2
3----3.06 Å2
Refinement stepCycle: 1 / Resolution: 2.1→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 45 41 1757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021752
X-RAY DIFFRACTIONr_bond_other_d0.0010.021546
X-RAY DIFFRACTIONr_angle_refined_deg1.861.9422361
X-RAY DIFFRACTIONr_angle_other_deg0.92733574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6925212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.03524.63482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28215235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.722153
X-RAY DIFFRACTIONr_chiral_restr0.1330.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021953
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
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_it3.2691.463866
X-RAY DIFFRACTIONr_mcbond_other3.1891.461865
X-RAY DIFFRACTIONr_mcangle_it4.452.1581072
X-RAY DIFFRACTIONr_mcangle_other4.4492.1581073
X-RAY DIFFRACTIONr_scbond_it6.0822.186886
X-RAY DIFFRACTIONr_scbond_other6.0792.188887
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2753.0241290
X-RAY DIFFRACTIONr_long_range_B_refined9.90818.641763
X-RAY DIFFRACTIONr_long_range_B_other9.90618.6581764
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 13 -
Rwork0.246 256 -
obs--22.25 %
Refinement TLS params.Method: refined / Origin x: 2.227 Å / Origin y: 169.466 Å / Origin z: 51.629 Å
111213212223313233
T0.0152 Å20.0058 Å20.0083 Å2-0.0129 Å2-0.0044 Å2--0.1359 Å2
L3.4419 °20.2766 °2-0.1895 °2-2.5082 °2-0.2218 °2--0.8068 °2
S0.0137 Å °0.1953 Å °-0.047 Å °-0.1838 Å °-0.0421 Å °-0.077 Å °0.0476 Å °0.012 Å °0.0284 Å °

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