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- PDB-3kco: Room temperature neutron structure of D-Xylose Isomerase in compl... -

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Basic information

Entry
Database: PDB / ID: 3kco
TitleRoom temperature neutron structure of D-Xylose Isomerase in complex with two Ni2+ cations and d12-D-glucose in the linear form (refined jointly with X-ray structure 3KBN)
ComponentsXylose isomerase
KeywordsISOMERASE / xylose isomerase / deuterated glucose / Carbohydrate metabolism / Metal-binding / Pentose shunt / Xylose metabolism
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
DEUTERATED WATER / D-glucose / NICKEL (II) ION / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKovalevsky, A.Y. / Langan, P.
CitationJournal: Structure / Year: 2010
Title: Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
Authors: Kovalevsky, A.Y. / Hanson, L. / Fisher, S.Z. / Mustyakimov, M. / Mason, S.A. / Forsyth, V.T. / Blakeley, M.P. / Keen, D.A. / Wagner, T. / Carrell, H.L. / Katz, A.K. / Glusker, J.P. / Langan, P.
History
DepositionOct 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Data collection
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_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l
Revision 1.5Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _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_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_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 21, 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
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6405
Polymers43,2831
Non-polymers3564
Water5,567309
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)174,55820
Polymers173,1334
Non-polymers1,42516
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 area35010 Å2
ΔGint-347 kcal/mol
Surface area46270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.007, 99.669, 102.862
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-1192-

DOD

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Components

#1: Protein Xylose isomerase /


Mass: 43283.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH / Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Sugar ChemComp-GLO / D-glucose / D-GLUCOSE IN LINEAR FORM / Glucose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#4: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: D2O
Source detailsTHE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 293 K / pH: 7.7
Details: 50MM HEPES, 40% v/v (NH4)2SO4 (sat.), protein 40 MG/ML, PH=7.7, BATCH METHOD, APO-XI CRYSTALS WERE SOAKED WITH 5mM NiCl2 SALT, 0.5M PER-DEUTERATED D-GLUCOSE IN D2O, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
NUCLEAR REACTORLANSCE PCS10.7-6.5
ROTATING ANODE21.54
Detector
TypeIDDetectorDate
TIME-OF-FLIGHT MULTIWIRE HE31AREA DETECTOROct 10, 2008
RIGAKU RAXIS IV++2IMAGE PLATEMar 10, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.71
26.51
31.541
ReflectionResolution: 1.8→20 Å / Num. all: 37568 / Num. obs: 27031 / % possible obs: 72 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.7 / Redundancy: 3.2 % / Rsym value: 0.236 / Net I/σ(I): 4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.359 / % possible all: 72.5

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Processing

Software
NameVersionClassification
PCSsoftwaredata collection
nCNSrefinement
d*TREKMODIFIED FOR NEUTRONdata reduction
LAUENORMMODIFIED FOR NEUTRONdata scaling
nCNSphasing
Refinement

% reflection Rfree: 5.1 % / R Free selection details: RANDOM / σ(F): 3 / Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 3CWH

3cwh

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection allNum. reflection obsDiffraction-IDStereochemistry target values
1.8-20NEUTRON DIFFRACTION0.2940.273138837568270311ENGH AND HUBER
1.53-20X-RAY DIFFRACTION0.2110.1993281
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 15 309 3378
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONc_bond_d0.007
NEUTRON DIFFRACTIONc_angle_deg1.011

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