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- PDB-6qrr: X-ray radiation dose series on xylose isomerase - 0.13 MGy -

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Basic information

Entry
Database: PDB / ID: 6qrr
TitleX-ray radiation dose series on xylose isomerase - 0.13 MGy
ComponentsXylose isomerase
KeywordsMETAL BINDING PROTEIN / Isomerase
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / 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
ISOPROPYL ALCOHOL / : / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.096 Å
AuthorsTaberman, H. / Bury, C.S. / van der Woerd, M.J. / Snell, E.H. / Garman, E.F.
Funding support Finland, 1items
OrganizationGrant numberCountry
Finnish Cultural Foundation Finland
CitationJournal: J.Synchrotron Radiat. / Year: 2019
Title: Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both.
Authors: Taberman, H. / Bury, C.S. / van der Woerd, M.J. / Snell, E.H. / Garman, E.F.
History
DepositionFeb 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.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 / _struct_conn.ptnr2_symmetry

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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)44,20520
Polymers43,1951
Non-polymers1,00919
Water9,476526
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)176,81980
Polymers172,7814
Non-polymers4,03876
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area47510 Å2
ΔGint-106 kcal/mol
Surface area41990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.478, 97.459, 102.485
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-408-

EDO

21A-601-

HOH

31A-926-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Xylose isomerase


Mass: 43195.277 Da / Num. of mol.: 1 / Mutation: E186Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / Production host: Escherichia coli (E. coli) / References: UniProt: P24300, xylose isomerase

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Non-polymers , 6 types, 545 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 2-propanol, ethylene glycol, HEPES, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.954, 0.855
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9541
20.8551
ReflectionResolution: 1.096→38.7 Å / Num. obs: 180192 / % possible obs: 95.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 10.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.072 / Net I/σ(I): 10.7
Reflection shellResolution: 1.096→1.135 Å / Rrim(I) all: 0.438

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIXv 1.14-3247-000refinement
SHELXLrefinement
XDSdata reduction
Aimlessdata scaling
ARP/wARPmodel building
Coot0.8.9.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MUW

1muw


Resolution: 1.096→38.69 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.147 --
Rwork0.121 --
obs-180192 95.7 %
Refinement stepCycle: LAST / Resolution: 1.096→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 58 526 3624

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