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Basic information

Entry
Database: PDB / ID: 2vha
TitleDEBP
ComponentsPERIPLASMIC BINDING TRANSPORT PROTEIN
KeywordsTRANSPORT PROTEIN / PERIPLASMIC BINDING PROTEIN / LIGAND BINDING / ULTRAHIGH RESOLUTION / STRUCTURAL BASIS OF STRUCTURAL BASIS OF SPECIFICITY / SHIGELLA FLEXNERI
Function / homology
Function and homology information


outer membrane-bounded periplasmic space
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1 Å
AuthorsHu, Y.L. / Fan, C.-P. / Fu, G.S. / Zhu, D.Y. / Jin, Q. / Wang, D.-C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structure of a Glutamate/Aspartate Binding Protein Complexed with a Glutamate Molecule: Structural Basis of Ligand Specificity at Atomic Resolution.
Authors: Hu, Y.L. / Fan, C.-P. / Fu, G.S. / Zhu, D.Y. / Jin, Q. / Wang, D.-C.
History
DepositionNov 20, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PERIPLASMIC BINDING TRANSPORT PROTEIN
B: PERIPLASMIC BINDING TRANSPORT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8516
Polymers64,3132
Non-polymers5394
Water13,151730
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-12.5 kcal/mol
Surface area29060 Å2
MethodPQS
Unit cell
Length a, b, c (Å)48.410, 68.180, 80.210
Angle α, β, γ (deg.)90.00, 98.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PERIPLASMIC BINDING TRANSPORT PROTEIN / PERIPLASMIC GLUTAMATE-ASPARTATE BINDING PROTEIN


Mass: 32156.457 Da / Num. of mol.: 2 / Fragment: RESIDUES 24-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHIGELLA FLEXNERI (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83S74, UniProt: A0A0H2UXX1*PLUS
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 730 / 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 Å3/Da / Density % sol: 39 % / Description: NONE

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 254360 / % possible obs: 92.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.5
Reflection shellResolution: 1→1.04 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / % possible all: 83.7

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Processing

Software
NameVersionClassification
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVERESOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1→10 Å / Num. parameters: 47109 / Num. restraintsaints: 57276 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1689 12707 5 %RANDOM
all0.1361 241338 --
obs--87.2 %-
Refine analyzeNum. disordered residues: 43 / Occupancy sum hydrogen: 4095.96 / Occupancy sum non hydrogen: 5099.28
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4320 0 36 730 5086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0293
X-RAY DIFFRACTIONs_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.041
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0.097

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