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- PDB-3b5j: Crystal Structures of the S504A Mutant of an Isolated ABC-ATPase ... -

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Basic information

Entry
Database: PDB / ID: 3b5j
TitleCrystal Structures of the S504A Mutant of an Isolated ABC-ATPase in Complex with TNP-ADP
ComponentsAlpha-hemolysin translocation ATP-binding protein hlyB
KeywordsTRANSPORT PROTEIN / ABC-TRANSPORTER / NUCLEOTIDE-BINDING DOAMIN / ATPase / ATP-binding / Hydrolase / Inner membrane / Membrane / Transmembrane
Function / homology
Function and homology information


type I protein secretion system complex / protein secretion by the type I secretion system / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
ATPase, type I secretion system, HlyB / Peptidase C39-like A / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily ...ATPase, type I secretion system, HlyB / Peptidase C39-like A / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-12D / Alpha-hemolysin translocation ATP-binding protein HlyB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsOswald, C. / Jenewein, S. / Smits, S.H.J. / Holland, I.B. / Schmitt, L.
CitationJournal: J.Struct.Biol. / Year: 2008
Title: Water-mediated protein-fluorophore interactions modulate the affinity of an ABC-ATPase/TNP-ADP complex
Authors: Oswald, C. / Jenewein, S. / Smits, S.H.J. / Holland, I.B. / Schmitt, L.
History
DepositionOct 26, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8232
Polymers27,1841
Non-polymers6381
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)179.200, 34.600, 38.000
Angle α, β, γ (deg.)90.000, 98.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-hemolysin translocation ATP-binding protein hlyB


Mass: 27184.260 Da / Num. of mol.: 1 / Fragment: ABC transporter, Residues UNP 467-707 / Mutation: S504A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hlyB / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P08716
#2: Chemical ChemComp-12D / 2',3'-O-[(1R,6R)-2,4,6-trinitrocyclohexa-2,4-diene-1,1-diyl]adenosine 5'-(trihydrogen diphosphate)


Mass: 638.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N8O16P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 14635 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.822 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.93
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.20.2913.56749359992.4
2.2-2.40.19554918257293.9
2.4-2.60.1456.83466182194.1
2.6-2.80.1218.42597134493.5
2.8-30.09210.11930102594.1
3-3.50.066133137161491.9
3.5-40.0517.5172488689.5
4-50.04319.5173088288.8
5-60.0418.678538887.6
6-100.03420.886040882.8
100.036221949664.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FF7

2ff7


Resolution: 2→17.98 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.888 / SU B: 11.481 / SU ML: 0.177 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1097 7.5 %RANDOM
Rwork0.204 ---
obs0.209 14625 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 mean: 39.359 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.04 Å2
2--0.09 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→17.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 42 261 2214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221986
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.9912691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3935242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9822490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46215360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7641516
X-RAY DIFFRACTIONr_chiral_restr0.0730.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021467
X-RAY DIFFRACTIONr_nbd_refined0.1930.2986
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21362
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2227
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.226
X-RAY DIFFRACTIONr_mcbond_it0.4611.51233
X-RAY DIFFRACTIONr_mcangle_it0.7721941
X-RAY DIFFRACTIONr_scbond_it1.0993880
X-RAY DIFFRACTIONr_scangle_it1.8914.5750
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 77 -
Rwork0.261 947 -
all-1024 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.34040.73480.0692.4804-0.18291.5352-0.01240.02820.05810.03590.04910.12770.1003-0.0356-0.0367-0.12150.0114-0.0073-0.2376-0.0127-0.189825.268-4.28920.785
28.7764-1.42332.15193.05820.34614.1838-0.3165-0.28510.7824-0.1751-0.06940.2459-0.4005-0.15380.3858-0.086-0.0085-0.2189-0.3025-0.01920.03848.2738.6617.842
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA465 - 5491 - 85
2X-RAY DIFFRACTION1AA625 - 707161 - 243
3X-RAY DIFFRACTION2AA550 - 62486 - 160

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