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- PDB-5j5u: Fjoh_4561 chitin-binding protein -

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Basic information

Entry
Database: PDB / ID: 5j5u
TitleFjoh_4561 chitin-binding protein
ComponentsRagB/SusD domain protein
KeywordsCHITIN-BINDING PROTEIN / Flavobacterium johnsoniae SusD homolog
Function / homologySusD-like 2 / Starch-binding associating with outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / RagB/SusD domain protein
Function and homology information
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKoropatkin, N.M.
CitationJournal: Biotechnol Biofuels / Year: 2016
Title: A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin.
Authors: Larsbrink, J. / Zhu, Y. / Kharade, S.S. / Kwiatkowski, K.J. / Eijsink, V.G. / Koropatkin, N.M. / McBride, M.J. / Pope, P.B.
History
DepositionApr 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RagB/SusD domain protein
B: RagB/SusD domain protein
C: RagB/SusD domain protein
D: RagB/SusD domain protein


Theoretical massNumber of molelcules
Total (without water)215,9084
Polymers215,9084
Non-polymers00
Water11,169620
1
A: RagB/SusD domain protein


Theoretical massNumber of molelcules
Total (without water)53,9771
Polymers53,9771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RagB/SusD domain protein


Theoretical massNumber of molelcules
Total (without water)53,9771
Polymers53,9771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RagB/SusD domain protein


Theoretical massNumber of molelcules
Total (without water)53,9771
Polymers53,9771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RagB/SusD domain protein


Theoretical massNumber of molelcules
Total (without water)53,9771
Polymers53,9771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.706, 82.885, 93.905
Angle α, β, γ (deg.)66.440, 78.330, 67.560
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 36 - 505 / Label seq-ID: 15 - 484

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

#1: Protein
RagB/SusD domain protein


Mass: 53976.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) (bacteria)
Strain: ATCC 17061 / DSM 2064 / UW101 / Gene: Fjoh_4561 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: A5FB55
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PegRx screen #2, condition 48: 3% Dextran sulfate sodium salt, 0.1 M Bicine pH 8.5, 15% Poly(ethylene) glycol 20,000
Temp details: room temp

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→44.49 Å / Num. obs: 181362 / % possible obs: 97.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.123 / Net I/av σ(I): 7.88 / Net I/σ(I): 7.88
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3061 / Mean I/σ(I) obs: 4.14 / % possible all: 96.68

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J90

5j90


Resolution: 2.3→44.49 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.83
RfactorNum. reflection% reflection
Rfree0.2626 3976 2.19 %
Rwork0.2139 --
obs0.215 181362 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.39 Å2 / Biso mean: 26.0173 Å2 / Biso min: 5.48 Å2
Refinement stepCycle: final / Resolution: 2.3→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14157 0 0 620 14777
Biso mean---25.32 -
Num. residues----1806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914500
X-RAY DIFFRACTIONf_angle_d1.13519653
X-RAY DIFFRACTIONf_chiral_restr0.0482057
X-RAY DIFFRACTIONf_plane_restr0.0062565
X-RAY DIFFRACTIONf_dihedral_angle_d13.1185226
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8573X-RAY DIFFRACTION3.515TORSIONAL
12B8573X-RAY DIFFRACTION3.515TORSIONAL
13C8573X-RAY DIFFRACTION3.515TORSIONAL
14D8573X-RAY DIFFRACTION3.515TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.32810.36611350.25636168630396
2.3281-2.35750.30661530.25266289644296
2.3575-2.38860.35571390.26036271641097
2.3886-2.42130.34921420.25726372651496
2.4213-2.45590.31831520.24876230638297
2.4559-2.49250.29891230.24086341646496
2.4925-2.53150.32561540.24926306646097
2.5315-2.5730.32371200.24946309642996
2.573-2.61730.32491700.2426273644396
2.6173-2.66490.26831120.24616374648697
2.6649-2.71620.29961430.24326236637996
2.7162-2.77160.27151570.23896403656097
2.7716-2.83180.34851290.24186298642797
2.8318-2.89770.27891410.23226328646997
2.8977-2.97020.31091640.2366413657797
2.9702-3.05040.24691280.22726317644597
3.0504-3.14020.29161160.2256354647097
3.1402-3.24150.33631620.22776327648997
3.2415-3.35730.24111320.22676389652197
3.3573-3.49170.26791480.22336319646797
3.4917-3.65050.20721460.21386340648697
3.6505-3.84290.23821360.19916403653997
3.8429-4.08350.24071460.18096378652498
4.0835-4.39860.20221430.16866425656897
4.3986-4.84070.1991540.16256368652298
4.8407-5.54010.22941360.17696398653498
5.5401-6.97550.20221510.1866399655098
6.9755-44.49780.22911440.19716358650297

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