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- PDB-4fso: Crystal Structure of Pseudomonas aeruginosa OccK10 (OpdN) -

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Basic information

Entry
Database: PDB / ID: 4fso
TitleCrystal Structure of Pseudomonas aeruginosa OccK10 (OpdN)
ComponentsProbable porin
KeywordsTRANSPORT PROTEIN / Beta-barrel / transporter (porin) / outer membrane
Function / homology
Function and homology information


porin activity / membrane
Similarity search - Function
Outer membrane porin, bacterial / outer membrane porin, OprD family / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsEren, E. / van den Berg, B.
CitationJournal: To be Published
Title: Crystal Structures of OccK Subfamily Proteins
Authors: Eren, E. / van den Berg, B.
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable porin
B: Probable porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,04513
Polymers91,2072
Non-polymers2,83811
Water1,08160
1
A: Probable porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,82910
Polymers45,6041
Non-polymers2,2259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2173
Polymers45,6041
Non-polymers6132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.872, 87.081, 98.177
Angle α, β, γ (deg.)90.00, 98.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable porin


Mass: 45603.691 Da / Num. of mol.: 2 / Fragment: unp residues 32-431
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA4179 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HWK2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / pH: 4
Details: 10% PEG 4000, 0.2M calcium chloride, 0.05M sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 25528 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rsym value: 0.076 / Net I/σ(I): 13
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.453 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3T20

3t20


Resolution: 2.75→14.8 Å / SU ML: 0.47 / σ(F): 1.36 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 1292 5.1 %
Rwork0.216 --
obs0.22 25350 99.6 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.61 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.947 Å20 Å2-1.1859 Å2
2---0.99 Å20 Å2
3----2.9569 Å2
Refinement stepCycle: LAST / Resolution: 2.75→14.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 0 122 60 5274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095293
X-RAY DIFFRACTIONf_angle_d1.37101
X-RAY DIFFRACTIONf_dihedral_angle_d19.141858
X-RAY DIFFRACTIONf_chiral_restr0.084734
X-RAY DIFFRACTIONf_plane_restr0.005939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7456-2.85480.37011470.29412610X-RAY DIFFRACTION98
2.8548-2.98370.35431420.26592673X-RAY DIFFRACTION100
2.9837-3.13960.31651310.23672680X-RAY DIFFRACTION100
3.1396-3.33420.30911430.21432648X-RAY DIFFRACTION99
3.3342-3.58820.26741430.21082650X-RAY DIFFRACTION100
3.5882-3.94310.3071410.21772706X-RAY DIFFRACTION100
3.9431-4.49960.2621540.19872669X-RAY DIFFRACTION100
4.4996-5.61710.26581400.18392698X-RAY DIFFRACTION100
5.6171-14.80290.26911510.22912724X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 30.8885 Å / Origin y: 26.2053 Å / Origin z: 26.8994 Å
111213212223313233
T0.0995 Å2-0.0121 Å20.0788 Å2--0.01 Å20.1361 Å2---0.0219 Å2
L0.2408 °20.0028 °20.0933 °2-0.3491 °2-0.0591 °2--0.8718 °2
S0.0427 Å °0.2653 Å °-0.0049 Å °-0.2705 Å °-0.1675 Å °0.0861 Å °-0.1253 Å °-0.0163 Å °0.0207 Å °
Refinement TLS groupSelection details: all

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