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- PDB-3psa: Classification of a Haemophilus influenzae ABC transporter HI1470... -

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Basic information

Entry
Database: PDB / ID: 3psa
TitleClassification of a Haemophilus influenzae ABC transporter HI1470/71 through its cognate molybdate periplasmic binding protein MolA (MolA bound to tungstate)
Componentsprotein HI_1472
KeywordsMETAL TRANSPORT / periplasmic binding protein / substrate binding protein / oxyanion binding protein
Function / homology
Function and homology information


monoatomic ion transport / cellular response to iron ion / periplasmic space
Similarity search - Function
ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TUNGSTATE(VI)ION / Molybdate-binding protein MolA
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsTirado-Lee, L. / Lee, A. / Rees, D.C. / Pinkett, H.W.
CitationJournal: Structure / Year: 2011
Title: Classification of a Haemophilus influenzae ABC Transporter HI1470/71 through Its Cognate Molybdate Periplasmic Binding Protein, MolA.
Authors: Tirado-Lee, L. / Lee, A. / Rees, D.C. / Pinkett, H.W.
History
DepositionDec 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: protein HI_1472
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8912
Polymers36,6431
Non-polymers2481
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.711, 122.711, 103.215
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein protein HI_1472 / periplasmic binding protein MolA


Mass: 36642.934 Da / Num. of mol.: 1 / Fragment: UNP residues 22-347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI_1472 / Production host: Escherichia coli (E. coli) / References: UniProt: P44206
#2: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: WO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 6.12 Å3/Da / Density % sol: 79.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 24% PEG2000 MME, 0.1 M sodium acetate, 0.2 M ammonium sulfate, 12% glycerol, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97856
SYNCHROTRONAPS 21-ID-D21.2143
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2010
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978561
21.21431
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.511
11-h,-k,l20.489
ReflectionResolution: 1.7→30 Å / Num. all: 99581 / Num. obs: 99140 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.074 / Χ2: 1.994 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.737.20.34896631.061100
1.73-1.767.40.30196051.0931100
1.76-1.797.40.27895821.0871100
1.79-1.837.40.24696371.1391100
1.83-1.877.50.20896571.191100
1.87-1.917.60.18896031.2631100
1.91-1.967.60.16595611.4011100
1.96-2.027.60.1596421.5381100
2.02-2.077.70.13796161.6931100
2.07-2.147.70.12196321.8371100
2.14-2.227.80.10596001.9591100
2.22-2.3180.09396071.9921100
2.31-2.418.10.08596492.0721100
2.41-2.548.30.08195942.3231100
2.54-2.78.50.07996202.711100
2.7-2.918.60.07496073.0191100
2.91-3.28.70.06596242.9861100
3.2-3.668.80.05296392.9191100
3.66-4.618.80.04695912.8141100
4.61-308.70.04596382.755199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.56 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.7 Å29.47 Å
Translation1.7 Å29.47 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→29.48 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.2356 / WRfactor Rwork: 0.2207 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8134 / SU B: 2.024 / SU ML: 0.063 / SU R Cruickshank DPI: 0.0145 / SU Rfree: 0.0146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 4868 4.9 %RANDOM
Rwork0.2189 ---
obs0.2198 99137 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.66 Å2 / Biso mean: 14.2862 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 5 139 2722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222638
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9733582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3495327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1125.574122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04115471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8671512
X-RAY DIFFRACTIONr_chiral_restr0.10.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211985
X-RAY DIFFRACTIONr_mcbond_it0.8191.51629
X-RAY DIFFRACTIONr_mcangle_it1.29622632
X-RAY DIFFRACTIONr_scbond_it2.3231009
X-RAY DIFFRACTIONr_scangle_it3.3884.5949
LS refinement shellResolution: 1.694→1.738 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 332 -
Rwork0.23 6547 -
all-6879 -
obs--94.4 %

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