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- PDB-2ia4: Crystal structure of Novel amino acid binding protein from Shigel... -

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Basic information

Entry
Database: PDB / ID: 2ia4
TitleCrystal structure of Novel amino acid binding protein from Shigella flexneri
ComponentsPutative periplasmic binding transport protein
KeywordsPROTEIN TRANSPORT / beta-alpha mixture
Function / homology
Function and homology information


amino acid transport / outer membrane-bounded periplasmic space / extracellular region
Similarity search - Function
: / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Periplasmic binding transport protein / Putative periplasmic binding transport protein
Similarity search - Component
Biological speciesShigella flexneri 2a str. 301 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsFan, C.P. / Wang, D.C.
CitationJournal: To be Published
Title: Structural and functional study of novel amino acid binding protein from Shigella flexneri
Authors: Fan, C.P. / Wang, D.C.
History
DepositionSep 7, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Putative periplasmic binding transport protein
B: Putative periplasmic binding transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6026
Polymers65,0632
Non-polymers5394
Water12,178676
1
A: Putative periplasmic binding transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8013
Polymers32,5321
Non-polymers2692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative periplasmic binding transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8013
Polymers32,5321
Non-polymers2692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.350, 67.710, 79.980
Angle α, β, γ (deg.)90.00, 98.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative periplasmic binding transport protein


Mass: 32531.609 Da / Num. of mol.: 2 / Fragment: residues 1-279
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a str. 301 (bacteria)
Species: Shigella flexneri / Strain: 2a 301 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q83S74, UniProt: A0A0H2UXX1*PLUS
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: trimethylamine N-oxide dihydrate, Polyethylene Glycol, Monomethyl ether 2000, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9500, 0.9794, 0.9799
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.97941
30.97991
ReflectionResolution: 1.5→50 Å / Num. all: 160587 / Num. obs: 154166 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 28.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 4 / Num. unique all: 8038 / Rsym value: 0.286 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→33.36 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 261723.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 14995 9.7 %RANDOM
Rwork0.2 ---
obs0.2 81248 96 %-
all-81329 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9813 Å2 / ksol: 0.338119 e/Å3
Displacement parametersBiso mean: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.5→33.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4339 0 36 676 5051
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 2333 9.7 %
Rwork0.282 21617 -
obs--89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3tris.paramtris.top

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