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- PDB-1zty: Crystal Structure of the Chitin Oligasaccharide Binding Protein -

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Basic information

Entry
Database: PDB / ID: 1zty
TitleCrystal Structure of the Chitin Oligasaccharide Binding Protein
ComponentsChitin Oligosaccharide Binding Protein
KeywordsSUGAR BINDING PROTEIN / SIGNALING PROTEIN / Alpha helix/beta sheet
Function / homology
Function and homology information


dipeptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptide ABC transporter, periplasmic peptide-binding protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsXu, S. / Li, X. / Roseman, R. / Stock, A.M.
CitationJournal: To be Published
Title: Crystal structure of the liganded and unliganded periplasmic Chitin oligosaccharide binding protein.
Authors: Xu, S. / Li, X. / Roseman, R. / Stock, A.M.
History
DepositionMay 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitin Oligosaccharide Binding Protein


Theoretical massNumber of molelcules
Total (without water)60,0171
Polymers60,0171
Non-polymers00
Water11,746652
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.813, 92.813, 137.029
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Chitin Oligosaccharide Binding Protein


Mass: 60017.105 Da / Num. of mol.: 1 / Fragment: residues 28-556
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Plasmid: pMal-p2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KUA3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.8 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, PEG400, HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97966, 0.97948, 0.97176
DetectorType: ENRAF-NONIUS / Detector: CCD / Date: Mar 23, 2004
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979661
20.979481
30.971761
ReflectionResolution: 2.3→50 Å / Num. all: 30939 / Num. obs: 30939 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 42.5 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 26.4
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 10.7 / Num. unique all: 3045 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 2130 -RANDOM
Rwork0.1941 ---
obs0.1941 30427 98.3 %-
all-30939 --
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4233 0 0 652 4885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.73
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.1

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