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- PDB-4xhc: rhamnosidase from Klebsiella oxytoca with rhamnose bound -

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Basic information

Entry
Database: PDB / ID: 4xhc
Titlerhamnosidase from Klebsiella oxytoca with rhamnose bound
ComponentsAlpha-L-rhamnosidase
KeywordsHYDROLASE
Function / homology
Function and homology information


alpha-L-rhamnosidase / alpha-L-rhamnosidase activity / catalytic activity
Similarity search - Function
Alpha-L-rhamnosidase, six-hairpin glycosidase domain / Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
alpha-L-rhamnopyranose / Alpha-L-rhamnosidase / Alpha-L-rhamnosidase
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsO'Neill, E.O. / Stevenson, C.E.M. / Patterson, M.J. / Rejzek, M. / Chauvin, A. / Lawson, D.M. / Field, R.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 United Kingdom
CitationJournal: Proteins / Year: 2015
Title: Crystal structure of a novel two domain GH78 family alpha-rhamnosidase from Klebsiella oxytoca with rhamnose bound.
Authors: O'Neill, E.C. / Stevenson, C.E. / Paterson, M.J. / Rejzek, M. / Chauvin, A.L. / Lawson, D.M. / Field, R.A.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 2, 2015Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: Alpha-L-rhamnosidase
B: Alpha-L-rhamnosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1268
Polymers123,4132
Non-polymers7136
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-44 kcal/mol
Surface area38360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.430, 148.430, 202.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 11 - 523 / Label seq-ID: 31 - 543

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Alpha-L-rhamnosidase


Mass: 61706.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N terminal tag was not cleaved prior to crystallisation
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: KOX_19945 / Plasmid: pET15b / Production host: Escherichia coli (E. coli)
References: UniProt: G8WCL1, UniProt: A0A0J9X262*PLUS, alpha-L-rhamnosidase
#2: Sugar ChemComp-RAM / alpha-L-rhamnopyranose / alpha-L-rhamnose / 6-deoxy-alpha-L-mannopyranose / L-rhamnose / rhamnose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-rhamnopyranoseCOMMON NAMEGMML 1.0
a-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 4.68 Å3/Da / Density % sol: 73.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% (w/v) PEG 3350, 200 mM MgSO4

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I2411.068
SYNCHROTRONDiamond I04-120.92
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJul 7, 2012
DECTRIS PILATUS 2M2PIXELDec 5, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0681
20.921
ReflectionRedundancy: 75.1 % / Number: 4618293 / Rmerge(I) obs: 0.177 / D res high: 2.7 Å / D res low: 92.58 Å / Num. obs: 61461 / % possible obs: 99.8 / Rejects: 3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
2.72.7711.66669.7
12.0792.5810.04867.1
ReflectionResolution: 2.7→63.07 Å / Num. obs: 61251 / % possible obs: 98.5 % / Redundancy: 4.9 % / Biso Wilson estimate: 41.8 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.061 / Net I/σ(I): 9.7 / Num. measured all: 300908
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.7-2.7751.0771.42205544500.6250.52299
12.07-63.074.50.0326.634247630.9980.01595.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SHELXphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→63.07 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1713 / WRfactor Rwork: 0.1569 / FOM work R set: 0.8296 / SU B: 20.257 / SU ML: 0.172 / SU R Cruickshank DPI: 0.292 / SU Rfree: 0.2117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 3084 5 %RANDOM
Rwork0.1823 58166 --
obs0.1833 58166 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.13 Å2 / Biso mean: 56.8 Å2 / Biso min: 31 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2---1.16 Å20 Å2
3---2.32 Å2
Refinement stepCycle: final / Resolution: 2.7→63.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8246 0 42 45 8333
Biso mean--71.28 44.7 -
Num. residues----1026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198516
X-RAY DIFFRACTIONr_bond_other_d0.0020.027858
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.93311618
X-RAY DIFFRACTIONr_angle_other_deg0.811317954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51851024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09523.084428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.812151302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1891574
X-RAY DIFFRACTIONr_chiral_restr0.0640.21256
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219740
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022158
X-RAY DIFFRACTIONr_mcbond_it1.2253.6484102
X-RAY DIFFRACTIONr_mcbond_other1.2253.6484101
X-RAY DIFFRACTIONr_mcangle_it1.9855.4725124
Refine LS restraints NCS

Ens-ID: 1 / Number: 32128 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 207 -
Rwork0.361 4236 -
all-4443 -
obs--98.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.71530.6443-0.28954.07290.40531.37360.2211-0.0824-0.02041.0216-0.02230.19560.3310.1403-0.19890.50190.0478-0.12390.19030.03250.184346.653920.092850.9845
21.88340.1799-0.22432.34521.1911.0992-0.02990.20360.1505-0.15930.2138-0.1357-0.12940.2653-0.18380.158-0.0217-0.07220.1332-0.01070.180850.058252.238438.1861
30.46650.75420.07272.48151.03211.3765-0.01-0.06590.00820.26120.1781-0.4460.17180.3841-0.16810.14250.059-0.18880.211-0.06310.285755.868433.734436.3288
41.4715-0.32070.19212.4382-0.00253.13820.0488-0.1086-0.37020.46750.0765-0.10150.45520.0284-0.12540.31110.0451-0.14060.01720.01030.199142.307510.525635.2679
55.71851.5598-1.77283.1505-1.09432.9382-0.11980.3397-0.1982-0.10740.1119-0.21330.35960.13750.00790.16420.0293-0.10010.0543-0.03990.12941.754210.911612.38
63.2063-0.5416-1.43322.82821.96611.84650.0540.22330.0304-0.1730.1573-0.3556-0.12750.1622-0.21140.13940.0318-0.10140.1979-0.02980.168851.8227.146421.5948
71.24241.43990.73093.62071.22621.2640.15030.1294-0.01630.40790.01420.09760.26190.0774-0.16450.1993-0.0030.04970.20850.0090.135335.000563.366263.0589
81.1295-0.743-0.143.05881.98522.2150.03520.0125-0.0590.2125-0.08260.26380.1302-0.05460.04740.1796-0.0656-0.03210.10530.00360.185627.231649.58952.1371
90.98750.445-0.19965.78220.86130.2094-0.11040.071-0.0153-0.1290.1287-0.01360.0471-0.0041-0.01830.2548-0.0277-0.06040.06820.02670.125433.284448.815350.6428
100.78350.43090.66371.52170.74270.95570.0431-0.2743-0.11630.5668-0.0040.08240.3557-0.1327-0.03920.37730.04540.02220.17870.01790.19333.909667.877470.1229
112.184-0.27551.37352.56090.65382.0490.0035-0.22840.24130.0962-0.03880.08870.0471-0.02440.03530.02-0.01780.01330.0665-0.05410.125438.42892.017767.6219
122.133-0.2487-1.3713.42431.70233.86310.0702-0.15590.12450.1748-0.12820.45640.1698-0.32530.05810.0278-0.0329-0.00130.1255-0.02930.162723.041878.522664.7417
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 33
2X-RAY DIFFRACTION2A34 - 164
3X-RAY DIFFRACTION3A165 - 242
4X-RAY DIFFRACTION4A243 - 381
5X-RAY DIFFRACTION5A382 - 441
6X-RAY DIFFRACTION6A442 - 523
7X-RAY DIFFRACTION7B11 - 57
8X-RAY DIFFRACTION8B58 - 125
9X-RAY DIFFRACTION9B126 - 168
10X-RAY DIFFRACTION10B169 - 259
11X-RAY DIFFRACTION11B260 - 441
12X-RAY DIFFRACTION12B442 - 523

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