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- PDB-4qdp: Joint X-ray and neutron structure of Streptomyces rubiginosus D-x... -

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Basic information

Entry
Database: PDB / ID: 4qdp
TitleJoint X-ray and neutron structure of Streptomyces rubiginosus D-xylose isomerase in complex with two Cd2+ ions and cyclic beta-L-arabinose
ComponentsXylose isomerase
KeywordsISOMERASE / TIM barrel / sugar isomerase / monosaccharides
Function / homology
Function and homology information


xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-L-arabinopyranose / : / DEUTERATED WATER / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKovalevsky, A.Y. / Langan, P.
CitationJournal: Structure / Year: 2014
Title: L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study.
Authors: Langan, P. / Sangha, A.K. / Wymore, T. / Parks, J.M. / Yang, Z.K. / Hanson, B.L. / Fisher, Z. / Mason, S.A. / Blakeley, M.P. / Forsyth, V.T. / Glusker, J.P. / Carrell, H.L. / Smith, J.C. / ...Authors: Langan, P. / Sangha, A.K. / Wymore, T. / Parks, J.M. / Yang, Z.K. / Hanson, B.L. / Fisher, Z. / Mason, S.A. / Blakeley, M.P. / Forsyth, V.T. / Glusker, J.P. / Carrell, H.L. / Smith, J.C. / Keen, D.A. / Graham, D.E. / Kovalevsky, A.
History
DepositionMay 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Apr 25, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.4Jun 20, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_monochromatic_or_laue_m_l
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6584
Polymers43,2831
Non-polymers3753
Water5,621312
1
A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,63316
Polymers173,1334
Non-polymers1,50012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Buried area34290 Å2
ΔGint-265 kcal/mol
Surface area46290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.930, 99.693, 102.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1152-

DOD

21A-1176-

DOD

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Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Sugar ChemComp-ARB / beta-L-arabinopyranose / beta-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArapbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-arabinopyranoseCOMMON NAMEGMML 1.0
b-L-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 291 K / Method: batch / pH: 7.7
Details: 0.1M HEPES, pH 7.7, 30% ammonium sulfate, batch, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12911
22911
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
NUCLEAR REACTORLANSCE PCS20.7-6.0
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEOct 10, 2011OSMIC VARIMAX
3He position sensitive detector2AREA DETECTOROct 20, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
20.71
361
Reflection

Entry-ID: 4QDP / Observed criterion σ(F): 2.5

Resolution (Å)Num. obs% possible obs (%)Observed criterion σ(I)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2-39.282878687.71.40.208229.3
1.6-406377399.97.10.055129
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obs% possible all
1.6-1.666.80.3795.3100
2-2.111.90.371.674

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Processing

Software
NameVersionClassificationNB
nCNS1.0.0refinement
d*TREKdata scaling
HKL-3000for X-raydata reduction
RETREATfor neutrondata reduction
HKL-3000for X-raydata scaling
RETREATfor neutrondata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Rfactor Rfree error: 0.003 / Cross valid method: FREE R-VALUE / σ(F): 2.5 / Stereochemistry target values: Joint X-ray/neutron ML
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1254 5 %random
Rwork0.231 ---
all0.231 28786 --
obs0.231 25245 --
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 59.3119 Å2 / ksol: 0.343945 e/Å3
Displacement parametersBiso max: 74.98 Å2 / Biso mean: 30.06 Å2 / Biso min: 16.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.09 Å
Luzzati d res high-1.6
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 12 312 3378
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_torsion_deg18.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.89
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.6-1.670.2442994.50.24162730.0147925657282.9
1.67-1.760.223444.90.20666830.0127919702788.7
1.76-1.870.1843554.80.1869880.017940734392.5
1.87-2.020.1933995.30.17571230.017926752294.9
2-2.090.3981115.30.419930.0384079210451.6
2.02-2.220.1723754.90.1873110.0097952768696.7
2.09-2.20.3661084.70.36322120.0354077232056.9
2.2-2.340.33613250.32225180.0294074265065
2.22-2.540.2013965.10.18374210.017993781797.8
2.34-2.520.2981404.60.28828710.0254103301173.4
2.52-2.770.28720260.26831390.024104334181.4
2.54-3.20.194205.30.17575070.0098034792798.7
2.77-3.170.2421885.10.22734990.0184118368789.5
3.17-3.990.18719650.17137590.0134140395595.5
3.2-19.890.17241050.15877340.0098265814498.5
3.99-19.720.18620750.16939700.0134301417797.1

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