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- PDB-1zhq: Crystal structure of apo MVL -

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Basic information

Entry
Database: PDB / ID: 1zhq
TitleCrystal structure of apo MVL
Componentsmannan-binding lectin
KeywordsSUGAR BINDING PROTEIN / HIV-1 / MVL / cyanobacteria / carbohydrate binding
Function / homology
Function and homology information


regulation of defense response to virus / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / carbohydrate binding / cytoplasm
Similarity search - Function
Dna Ligase; domain 1 - #230 / Mannan-binding protein / : / Mannan-binding protein / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Lectin MVL
Similarity search - Component
Biological speciesMicrocystis viridis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsWilliams, D.C. / Lee, J.Y. / Cai, M. / Bewley, C.A. / Clore, G.M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structures of the HIV-1 Inhibitory Cyanobacterial Protein MVL Free and Bound to Man3GlcNAc2: STRUCTURAL BASIS FOR SPECIFICITY AND HIGH-AFFINITY BINDING TO THE CORE PENTASACCHARIDE FROM ...Title: Crystal Structures of the HIV-1 Inhibitory Cyanobacterial Protein MVL Free and Bound to Man3GlcNAc2: STRUCTURAL BASIS FOR SPECIFICITY AND HIGH-AFFINITY BINDING TO THE CORE PENTASACCHARIDE FROM N-LINKED OLIGOMANNOSIDE.
Authors: Williams, D.C. / Lee, J.Y. / Cai, M. / Bewley, C.A. / Clore, G.M.
History
DepositionApr 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: mannan-binding lectin
B: mannan-binding lectin
C: mannan-binding lectin
D: mannan-binding lectin
E: mannan-binding lectin
F: mannan-binding lectin
G: mannan-binding lectin
H: mannan-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,33427
Polymers97,9578
Non-polymers1,37719
Water15,583865
1
A: mannan-binding lectin
B: mannan-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,18011
Polymers24,4892
Non-polymers6909
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-33 kcal/mol
Surface area10390 Å2
MethodPISA
2
C: mannan-binding lectin
D: mannan-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7085
Polymers24,4892
Non-polymers2193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-30 kcal/mol
Surface area10210 Å2
MethodPISA
3
E: mannan-binding lectin
F: mannan-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8337
Polymers24,4892
Non-polymers3435
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-37 kcal/mol
Surface area10370 Å2
MethodPISA
4
G: mannan-binding lectin
H: mannan-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6134
Polymers24,4892
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-26 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.184, 74.873, 83.901
Angle α, β, γ (deg.)90.00, 100.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
mannan-binding lectin / MVL


Mass: 12244.663 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis viridis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RHG4
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 865 / 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: 2.401 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Ammonium dihydrogen phosphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 73335 / Num. obs: 71428 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.092
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.25 / Num. unique all: 6946 / % possible all: 95.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→19.87 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 460807.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 6949 10.1 %RANDOM
Rwork0.177 ---
all0.177 73061 --
obs0.177 68726 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.0686 Å2 / ksol: 0.368284 e/Å3
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å20 Å2-3.1 Å2
2---2.23 Å20 Å2
3----0.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6920 0 82 865 7867
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.552
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 1015 9.6 %
Rwork0.233 9513 -
obs--87 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5egl.paregl.top

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