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- PDB-2nq2: An inward-facing conformation of a putative metal-chelate type AB... -

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Basic information

Entry
Database: PDB / ID: 2nq2
TitleAn inward-facing conformation of a putative metal-chelate type ABC transporter.
Components
  • Hypothetical ABC transporter ATP-binding protein HI1470
  • Hypothetical ABC transporter permease protein HI1471
KeywordsMETAL TRANSPORT / putative iron chelatin ABC transporter / ATP-binding protein / nucleotide binding domain / transmembrane domain
Function / homology
Function and homology information


ABC-type molybdate transporter / ABC-type molybdate transporter activity / siderophore-dependent iron import into cell / plasma membrane => GO:0005886 / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding
Similarity search - Function
ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter, BtuC-like / 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. ...ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter, BtuC-like / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Molybdate import system permease protein MolB / Molybdate import ATP-binding protein MolC
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsPinkett, H.P. / Lee, A.T. / Lum, P. / Locher, K.P. / Rees, D.C.
CitationJournal: Science / Year: 2007
Title: An inward-facing conformation of a putative metal-chelate-type ABC transporter.
Authors: Pinkett, H.W. / Lee, A.T. / Lum, P. / Locher, K.P. / Rees, D.C.
History
DepositionOct 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical ABC transporter permease protein HI1471
C: Hypothetical ABC transporter ATP-binding protein HI1470
B: Hypothetical ABC transporter permease protein HI1471
D: Hypothetical ABC transporter ATP-binding protein HI1470


Theoretical massNumber of molelcules
Total (without water)130,2014
Polymers130,2014
Non-polymers00
Water12,286682
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-102 kcal/mol
Surface area44500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.846, 142.465, 150.268
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer

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Components

#1: Protein Hypothetical ABC transporter permease protein HI1471


Mass: 36553.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: KW20 Rd / Gene: HI_1471 / Plasmid: pET19b/pET21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/B834(DE3) / References: UniProt: Q57130
#2: Protein Hypothetical ABC transporter ATP-binding protein HI1470


Mass: 28546.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: KW20 Rd / Gene: HI_1470 / Plasmid: pET19b/pET21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/B834(DE3) / References: UniProt: Q57399
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.07 Å3/Da / Density % sol: 69.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 34% pentaerythritol propoxylate, 0.1M sodium citrate, pH 5.5, 0.2M potassium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)Wavelength
SYNCHROTRONSSRL BL9-210.97925, 0.89194, 0.97927
SYNCHROTRONSSRL BL9-220.97927
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 16, 2005 / Details: mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromatorMADMx-ray1
2Double crystal monochromatorSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.891941
30.979271
ReflectionResolution: 2.4→30 Å / Num. all: 82485 / Num. obs: 82020 / % possible obs: 99.5 % / Redundancy: 14.5 % / Biso Wilson estimate: 31.4 Å2 / Rsym value: 0.061 / Net I/σ(I): 16.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 14.1 % / Num. unique all: 11759 / Rsym value: 0.27 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→28 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Water molecules positioned in the membrane spanning region likely correspond to density from disordered detergents and possibly associated phospholipids.
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 8214 9.8 %RANDOM
Rwork0.2224 ---
all-81824 --
obs-81106 98.9 %-
Solvent computationBsol: 50.067 Å2
Displacement parametersBiso mean: 51.093 Å2
Baniso -1Baniso -2Baniso -3
1-5.304 Å20 Å20 Å2
2---4.449 Å20 Å2
3----0.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8569 0 0 682 9251
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.185
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.008
RfactorNum. reflection
Rfree0.302 1297
Rwork0.249 -
obs-11759
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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