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- PDB-3jty: Crystal structure of a BenF-like porin from Pseudomonas fluoresce... -

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Basic information

Entry
Database: PDB / ID: 3jty
TitleCrystal structure of a BenF-like porin from Pseudomonas fluorescens Pf-5
ComponentsBenF-like porin
KeywordsTRANSPORT PROTEIN / PFL_1329 / BenF-like porin / Pseudomonas fluorescens Pf-5 / BENZOATE TRANSPORTER / EFFLUX PUMP / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homologyOuter membrane porin, bacterial / outer membrane porin, OprD family / Porin / Porin domain superfamily / Porin / membrane => GO:0016020 / Beta Barrel / Mainly Beta / Outer membrane porin, OprD family
Function and homology information
Biological speciesPseudomonas fluorescens Pf-5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 Å
AuthorsSampathkumar, P. / Lu, F. / Zhao, X. / Wasserman, S. / Iuzuka, M. / Bain, K. / Rutter, M. / Gheyi, T. / Atwell, S. / Luz, J. ...Sampathkumar, P. / Lu, F. / Zhao, X. / Wasserman, S. / Iuzuka, M. / Bain, K. / Rutter, M. / Gheyi, T. / Atwell, S. / Luz, J. / Gilmore, J. / Sauder, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proteins / Year: 2010
Title: Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution.
Authors: Sampathkumar, P. / Lu, F. / Zhao, X. / Li, Z. / Gilmore, J. / Bain, K. / Rutter, M.E. / Gheyi, T. / Schwinn, K.D. / Bonanno, J.B. / Pieper, U. / Fajardo, J.E. / Fiser, A. / Almo, S.C. / ...Authors: Sampathkumar, P. / Lu, F. / Zhao, X. / Li, Z. / Gilmore, J. / Bain, K. / Rutter, M.E. / Gheyi, T. / Schwinn, K.D. / Bonanno, J.B. / Pieper, U. / Fajardo, J.E. / Fiser, A. / Almo, S.C. / Swaminathan, S. / Chance, M.R. / Baker, D. / Atwell, S. / Thompson, D.A. / Emtage, J.S. / Wasserman, S.R. / Sali, A. / Sauder, J.M. / Burley, S.K.
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BenF-like porin
B: BenF-like porin
C: BenF-like porin
D: BenF-like porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,4176
Polymers178,9584
Non-polymers4592
Water45025
1
A: BenF-like porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9692
Polymers44,7401
Non-polymers2291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BenF-like porin


Theoretical massNumber of molelcules
Total (without water)44,7401
Polymers44,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BenF-like porin


Theoretical massNumber of molelcules
Total (without water)44,7401
Polymers44,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BenF-like porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9692
Polymers44,7401
Non-polymers2291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.103, 210.624, 84.066
Angle α, β, γ (deg.)90.000, 97.760, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 32 - 419 / Label seq-ID: 6 - 393

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
BenF-like porin


Mass: 44739.523 Da / Num. of mol.: 4 / Fragment: Residues 30 -420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens Pf-5 (bacteria)
Strain: Pf-5 / ATCC BAA-477 / Gene: PFL_1329, PFL_1329; Q4KH25_PSEF5 / Plasmid: BC-pSGX3(BC); modified pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: Q4KH25
#2: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 100mM Citric acid, 21% PEG 3350, 10% w/v ANAPOE-X-114 from the detergent screen, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 31, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.58→53.68 Å / Num. obs: 67053 / % possible obs: 100 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.14 Å2 / Rsym value: 0.14 / Net I/σ(I): 6.1
Reflection shellResolution: 2.58→2.72 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 9774 / Rsym value: 0.527 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.76 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.58 Å35.1 Å
Translation2.58 Å35.1 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.1.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Poly-Alanine model of the PDB code 2QTK

2qtk


Resolution: 2.58→35.11 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.865 / WRfactor Rfree: 0.275 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.777 / SU B: 11.28 / SU ML: 0.253 / SU R Cruickshank DPI: 0.499 / SU Rfree: 0.312 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.499 / ESU R Free: 0.312
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; NCS restraints used.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 3390 5.1 %RANDOM
Rwork0.22 ---
obs0.222 66977 100 %-
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 max: 85.14 Å2 / Biso mean: 41.96 Å2 / Biso min: 19.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.02 Å2
2---0.05 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.58→35.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11859 0 32 25 11916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02112158
X-RAY DIFFRACTIONr_bond_other_d0.0010.028181
X-RAY DIFFRACTIONr_angle_refined_deg1.61.93316435
X-RAY DIFFRACTIONr_angle_other_deg0.95319754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2251532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06424.132593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.559151897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0131574
X-RAY DIFFRACTIONr_chiral_restr0.0940.21714
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022699
X-RAY DIFFRACTIONr_nbd_refined0.1910.21685
X-RAY DIFFRACTIONr_nbd_other0.2060.27863
X-RAY DIFFRACTIONr_nbtor_refined0.1840.25276
X-RAY DIFFRACTIONr_nbtor_other0.0870.26888
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2303
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.22
X-RAY DIFFRACTIONr_mcbond_it0.7371.57819
X-RAY DIFFRACTIONr_mcbond_other0.1621.53207
X-RAY DIFFRACTIONr_mcangle_it1.26211935
X-RAY DIFFRACTIONr_scbond_it1.55135163
X-RAY DIFFRACTIONr_scangle_it2.2024.54500
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 4935 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.40.5
BMEDIUM POSITIONAL0.380.5
CMEDIUM POSITIONAL0.370.5
DMEDIUM POSITIONAL0.370.5
AMEDIUM THERMAL0.622
BMEDIUM THERMAL0.62
CMEDIUM THERMAL0.592
DMEDIUM THERMAL0.632
LS refinement shellResolution: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 226 -
Rwork0.277 4677 -
all-4903 -
obs--100 %

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