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- PDB-1a99: PUTRESCINE RECEPTOR (POTF) FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1a99
TitlePUTRESCINE RECEPTOR (POTF) FROM E. COLI
ComponentsPUTRESCINE-BINDING PROTEIN
KeywordsBINDING PROTEIN / TRANSPORT / PERIPLASMIC PUTRESCINE BINDING PROTEIN (POTF)
Function / homology
Function and homology information


putrescine transport / putrescine binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Spermidine/putrescine-binding periplasmic protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIAMINOBUTANE / Putrescine-binding periplasmic protein PotF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsVassylyev, D.G. / Tomitori, H. / Kashiwagi, K. / Morikawa, K. / Igarashi, K.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificity.
Authors: Vassylyev, D.G. / Tomitori, H. / Kashiwagi, K. / Morikawa, K. / Igarashi, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and Preliminary X-Ray Analysis of the Periplasmic Receptor (Potf) of the Putrescine Transport System in Escherichia Coli
Authors: Vassylyev, D.G. / Kashiwagi, T. / Tomitori, H. / Kashiwagi, K. / Igarashi, K. / Morikawa, K.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Characteristics of the Operon for a Putrescine Transport System that Maps at 19 Minutes on the Escherichia Coli Chromosome
Authors: Pistocchi, R. / Kashiwagi, K. / Miyamoto, S. / Nukui, E. / Sadakata, Y. / Kobayashi, H. / Igarashi, K.
History
DepositionApr 17, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 1, 2020Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_distant_solvent_atoms ...pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTRESCINE-BINDING PROTEIN
B: PUTRESCINE-BINDING PROTEIN
C: PUTRESCINE-BINDING PROTEIN
D: PUTRESCINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,5508
Polymers153,1984
Non-polymers3534
Water10,521584
1
A: PUTRESCINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3882
Polymers38,2991
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PUTRESCINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3882
Polymers38,2991
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PUTRESCINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3882
Polymers38,2991
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PUTRESCINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3882
Polymers38,2991
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)269.400, 82.330, 93.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7942, 0.59665, -0.1151), (0.46434, 0.47372, -0.74832), (-0.39196, -0.64777, -0.65328)289.24081, -14.83522, 190.97041
2given(0.93969, 0.13875, -0.31261), (0.11935, -0.98959, -0.08045), (-0.32052, 0.03828, -0.94647)31.41611, 65.41694, 155.36401
3given(-0.87784, 0.47572, 0.05558), (-0.27243, -0.59138, 0.75898), (0.39393, 0.65112, 0.64874)297.77582, 60.40127, -92.03163

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Components

#1: Protein
PUTRESCINE-BINDING PROTEIN / POTF


Mass: 38299.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: KK313 / Cellular location: PERIPLASM / Gene: PUCPOTF / Plasmid: PMWPOTF / Gene (production host): PUCPOTF / Production host: Escherichia coli (E. coli) / Strain (production host): KK313POTF\:\:KM / References: UniProt: P31133
#2: Chemical
ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE / Putrescine


Mass: 88.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12N2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 60 %
Crystal growpH: 5
Details: PROTEIN WAS CRYSTALLIZED FROM 2M AMMONIUM SULFATE, 6% GLYCEROL, 200MM CACODYLATE BUFFER (PH 5), pH 5.0
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Details: Vassylyev, D.G., (1998) Acta Crystallogr.,Sect.D, 54, 132.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
220 mMTris-HCl1drop
42.5 Mammonium sulfate1reservoir
56 %glycerol1reservoir
6200 mMcacodylate1reservoir
31drop0.00125mlH2O

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Data collection

RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 40 Å2
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. obs: 87495 / % possible obs: 94 % / Num. measured all: 273045 / Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementResolution: 2.2→30 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 4618 5 %RANDOM
Rwork0.185 ---
obs0.185 91992 87 %-
Displacement parametersBiso mean: 38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-6 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11308 0 24 584 11916
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.852
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.31.5
X-RAY DIFFRACTIONx_mcangle_it62
X-RAY DIFFRACTIONx_scbond_it7.12
X-RAY DIFFRACTIONx_scangle_it92.5
Refine LS restraints NCSNCS model details: RESTRAINED / Rms dev Biso : 6.5 Å2 / Rms dev position: 1 Å / Weight Biso : 1 / Weight position: 100
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.349 344 5 %
Rwork0.332 6513 -
obs--47 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 90790 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.49

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