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- PDB-5ngw: Glycoside hydrolase-like protein -

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Basic information

Entry
Database: PDB / ID: 5ngw
TitleGlycoside hydrolase-like protein
ComponentsOpGH99A
KeywordsHYDROLASE / Glycoside hydrolase / Flavobacteria / Marine polysaccharide
Function / homologyBROMIDE ION / OpGH99A
Function and homology information
Biological speciesFlavobacteriaceae bacterium S85 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRobb, C.S. / Hehemann, J.-H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Protein Sci. / Year: 2017
Title: Crystal structure of a marine glycoside hydrolase family 99-related protein lacking catalytic machinery.
Authors: Robb, C.S. / Mystkowska, A.A. / Hehemann, J.H.
History
DepositionMar 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OpGH99A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6266
Polymers44,2271
Non-polymers4005
Water2,774154
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-0 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.054, 102.054, 80.113
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein OpGH99A


Mass: 44226.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacteriaceae bacterium S85 (bacteria)
Gene: ZP09498382.1 / Plasmid: pET28
Details (production host): Kanamycin resistance, T7 expression
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R2JFJ2*PLUS
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 100 mM Tris pH 8.0 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→88.38 Å / Num. obs: 19223 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Net I/σ(I): 13.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 3 / Num. unique obs: 2761 / CC1/2: 0.86 / Rpim(I) all: 0.25 / Rsym value: 0.783 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4acy

4acy


Resolution: 2.4→88.38 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.622 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.213 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21468 1011 5.3 %RANDOM
Rwork0.16386 ---
obs0.16644 18190 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.336 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20.51 Å20 Å2
2--1.01 Å2-0 Å2
3----3.29 Å2
Refinement stepCycle: 1 / Resolution: 2.4→88.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 5 154 3005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022920
X-RAY DIFFRACTIONr_bond_other_d0.0020.022624
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9333980
X-RAY DIFFRACTIONr_angle_other_deg0.99635997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15625.097155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84615436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4811512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213469
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02741
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.44.731439
X-RAY DIFFRACTIONr_mcbond_other3.3934.7281438
X-RAY DIFFRACTIONr_mcangle_it4.8487.0811797
X-RAY DIFFRACTIONr_mcangle_other4.8477.0831798
X-RAY DIFFRACTIONr_scbond_it3.9594.8811481
X-RAY DIFFRACTIONr_scbond_other3.9584.8831482
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6077.2422184
X-RAY DIFFRACTIONr_long_range_B_refined6.86537.8253494
X-RAY DIFFRACTIONr_long_range_B_other6.86637.7173441
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 56 -
Rwork0.241 1348 -
obs--100 %

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