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- PDB-3wiw: Crystal structure of unsaturated glucuronyl hydrolase specific fo... -

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Basic information

Entry
Database: PDB / ID: 3wiw
TitleCrystal structure of unsaturated glucuronyl hydrolase specific for heparin
ComponentsGlycosyl hydrolase family 88
KeywordsHYDROLASE / alpha6/alpha6-barrel
Function / homology
Function and homology information


Glycosyl hydrolase, family 88 / Glycosyl Hydrolase Family 88 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Glycosyl hydrolase family 88
Similarity search - Component
Biological speciesPedobacter heparinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsNakamichi, Y. / Mikami, B. / Murata, K. / Hashimoto, W.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal structure of a bacterial unsaturated glucuronyl hydrolase with specificity for heparin.
Authors: Nakamichi, Y. / Mikami, B. / Murata, K. / Hashimoto, W.
History
DepositionSep 26, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations / Category: citation / database_2 / struct_site
Item: _citation.journal_id_CSD / _citation.journal_volume ..._citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl hydrolase family 88
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9182
Polymers45,6801
Non-polymers2381
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.840, 50.960, 85.816
Angle α, β, γ (deg.)90.00, 115.73, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-844-

HOH

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Components

#1: Protein Glycosyl hydrolase family 88


Mass: 45679.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pedobacter heparinus (bacteria) / Strain: ATCC 13125 / DSM 2366 / NCIB 9290 / Gene: Phep_2830 / Plasmid: pCold-IV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B / References: UniProt: C6Y1N7
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 1.98 Å3/Da / Density % sol: 37.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG6000, 0.1M HEPES-Na, 0.1M lithium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2013
RadiationMonochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 78862 / Num. obs: 78862 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 32.5
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.72 / Num. unique all: 7783 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZZR

2zzr


Resolution: 1.35→45.634 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 15.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1598 2001 2.54 %RANDOM
Rwork0.1318 ---
obs0.1325 78821 99.67 %-
all-78821 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.7 Å2
Refinement stepCycle: LAST / Resolution: 1.35→45.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 15 422 3447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093364
X-RAY DIFFRACTIONf_angle_d1.2264593
X-RAY DIFFRACTIONf_dihedral_angle_d13.0341251
X-RAY DIFFRACTIONf_chiral_restr0.084469
X-RAY DIFFRACTIONf_plane_restr0.007595
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.35-1.38030.21351350.1491530497
1.3803-1.41760.22171500.14165480100
1.4176-1.45930.17381290.12915497100
1.4593-1.50640.15161570.11745436100
1.5064-1.56030.17731410.10785469100
1.5603-1.62270.18671350.10455479100
1.6227-1.69660.16151450.10395518100
1.6966-1.7860.14581560.11025473100
1.786-1.89790.17111350.11575500100
1.8979-2.04450.14741400.12215506100
2.0445-2.25020.14631470.12575469100
2.2502-2.57580.17211410.13955517100
2.5758-3.24510.15651450.15295561100
3.2451-45.66060.14961450.1386561199

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