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- PDB-4gcp: Crystal Structure of E. coli OmpF porin in complex with Ampicillin -

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Basic information

Entry
Database: PDB / ID: 4gcp
TitleCrystal Structure of E. coli OmpF porin in complex with Ampicillin
ComponentsOuter membrane protein F
KeywordsMEMBRANE PROTEIN/ANTIBIOTIC / Beta-barrel / Protein-drug complex / Trimer / Non-specific Channel / Ampicillin binding / Outer membrane / MEMBRANE PROTEIN-ANTIBIOTIC complex
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 / : / Porin domain superfamily / Porin ...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 / : / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-AIC / Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsZiervogel, B.K. / Roux, B.
CitationJournal: Structure / Year: 2013
Title: The Binding of Antibiotics in OmpF Porin.
Authors: Ziervogel, B.K. / Roux, B.
History
DepositionJul 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: 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 / struct_ncs_dom_lim / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein F
B: Outer membrane protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0414
Polymers74,3432
Non-polymers6992
Water4,738263
1
A: Outer membrane protein F
hetero molecules

A: Outer membrane protein F
hetero molecules

A: Outer membrane protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5626
Polymers111,5143
Non-polymers1,0483
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 area9330 Å2
ΔGint-43 kcal/mol
Surface area40460 Å2
MethodPISA
2
B: Outer membrane protein F
hetero molecules

B: Outer membrane protein F
hetero molecules

B: Outer membrane protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5626
Polymers111,5143
Non-polymers1,0483
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9360 Å2
ΔGint-40 kcal/mol
Surface area40500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.600, 116.600, 53.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

21B-617-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth seq-ID: 8 - 340 / Label seq-ID: 9 - 341

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Outer membrane protein F / Outer membrane protein 1A / Outer membrane protein B / Outer membrane protein IA / Porin OmpF


Mass: 37171.301 Da / Num. of mol.: 2 / Fragment: UNP Residues 23-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ompF, cmlB, coa, cry, tolF, b0929, JW0912 / Production host: Escherichia coli (E. coli) / References: UniProt: P02931
#2: Chemical ChemComp-AIC / (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / AMPICILLIN / D(-)-ALPHA-AMINOBENZYLPENICILLIN / 6-[D(-)-ALPHA-AMINOPHENYLLACETAMIDO]PENICILLANIC ACID


Mass: 349.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19N3O4S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50% PEG 200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2011
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 56274 / Num. obs: 55640 / % possible obs: 98.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.8
Reflection shell% possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERv2.1phasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→47.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.734 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.171 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23916 2836 5.1 %RANDOM
Rwork0.20312 ---
obs0.20494 52782 98.61 %-
all-53525 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.694 Å2
Baniso -1Baniso -2Baniso -3
1--2.84 Å2-1.42 Å20 Å2
2---2.84 Å20 Å2
3---4.26 Å2
Refinement stepCycle: LAST / Resolution: 1.98→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5136 0 48 263 5447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225262
X-RAY DIFFRACTIONr_angle_refined_deg2.061.9377148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9795668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31824.786280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87915730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1961522
X-RAY DIFFRACTIONr_chiral_restr0.1490.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024266
X-RAY DIFFRACTIONr_mcbond_it1.1351.53254
X-RAY DIFFRACTIONr_mcangle_it1.94225128
X-RAY DIFFRACTIONr_scbond_it2.91632008
X-RAY DIFFRACTIONr_scangle_it4.3094.52016
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2548 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.040.05
tight thermal0.160.5
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 211 -
Rwork0.291 3845 -
obs--98.11 %

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