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- PDB-6qrx: X-ray radiation dose series on xylose isomerase - 3.88 MGy -

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Basic information

Entry
Database: PDB / ID: 6qrx
TitleX-ray radiation dose series on xylose isomerase - 3.88 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: 1.17 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 / refine / 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 / _refine.pdbx_diffrn_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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

Downloads & links

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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 area47130 Å2
ΔGint-86 kcal/mol
Surface area42780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.612, 97.636, 102.598
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-408-

EDO

21A-587-

HOH

31A-937-

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
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 / Comment: alkaloid*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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: 2.68 Å3/Da / Density % sol: 54.18 %
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: 1.17→38.75 Å / Num. obs: 154713 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rrim(I) all: 0.09 / Net I/σ(I): 9.9
Reflection shellResolution: 1.17→1.19 Å / Rrim(I) all: 0.847

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Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QRR

6qrr


Resolution: 1.17→38.741 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.45
RfactorNum. reflection% reflection
Rfree0.1282 7727 4.99 %
Rwork0.1086 --
obs0.1096 154705 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.17→38.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 58 526 3624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093755
X-RAY DIFFRACTIONf_angle_d1.1535132
X-RAY DIFFRACTIONf_dihedral_angle_d15.241450
X-RAY DIFFRACTIONf_chiral_restr0.081511
X-RAY DIFFRACTIONf_plane_restr0.009716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.18330.29132440.27494675X-RAY DIFFRACTION96
1.1833-1.19720.29432490.26224769X-RAY DIFFRACTION97
1.1972-1.21180.27622580.23564849X-RAY DIFFRACTION99
1.2118-1.22720.23722550.20854893X-RAY DIFFRACTION99
1.2272-1.24330.21722580.18594846X-RAY DIFFRACTION100
1.2433-1.26040.1742550.16414876X-RAY DIFFRACTION100
1.2604-1.27840.18022550.16394870X-RAY DIFFRACTION100
1.2784-1.29740.18382580.15254885X-RAY DIFFRACTION100
1.2974-1.31770.15372570.13874913X-RAY DIFFRACTION100
1.3177-1.33930.13892590.12994887X-RAY DIFFRACTION100
1.3393-1.36240.14462560.12714898X-RAY DIFFRACTION100
1.3624-1.38720.15532570.12474933X-RAY DIFFRACTION100
1.3872-1.41390.15352580.12424869X-RAY DIFFRACTION100
1.4139-1.44270.1342570.10814903X-RAY DIFFRACTION100
1.4427-1.47410.11782580.09314885X-RAY DIFFRACTION100
1.4741-1.50840.10362570.08414938X-RAY DIFFRACTION100
1.5084-1.54610.11052580.08214882X-RAY DIFFRACTION100
1.5461-1.58790.12072600.08144927X-RAY DIFFRACTION100
1.5879-1.63470.09382570.07684913X-RAY DIFFRACTION100
1.6347-1.68740.09932600.07764931X-RAY DIFFRACTION100
1.6874-1.74770.10272600.08194926X-RAY DIFFRACTION100
1.7477-1.81770.10012580.08194921X-RAY DIFFRACTION100
1.8177-1.90040.10232600.08884913X-RAY DIFFRACTION100
1.9004-2.00060.10252600.0884948X-RAY DIFFRACTION100
2.0006-2.1260.10472610.09164949X-RAY DIFFRACTION100
2.126-2.29010.10012580.09024950X-RAY DIFFRACTION100
2.2901-2.52050.11122610.09184942X-RAY DIFFRACTION100
2.5205-2.88510.11792610.09744996X-RAY DIFFRACTION99
2.8851-3.63450.12992620.10544999X-RAY DIFFRACTION99
3.6345-38.76270.14592600.12974892X-RAY DIFFRACTION94

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