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- PDB-7cjp: Crystal structure of metal-free state of glucose isomerase -

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Basic information

Entry
Database: PDB / ID: 7cjp
TitleCrystal structure of metal-free state of glucose isomerase
ComponentsXylose isomerase
KeywordsISOMERASE / glucose isomerase / metal-free state
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. / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017R1D1A1B03033087 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structure of the metal-free state of glucose isomerase reveals its minimal open configuration for metal binding.
Authors: Nam, K.H.
History
DepositionJul 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylose isomerase
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,99425
Polymers86,5672
Non-polymers1,42823
Water11,422634
1
A: Xylose isomerase
B: Xylose isomerase
hetero molecules

A: Xylose isomerase
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,98850
Polymers173,1334
Non-polymers2,85546
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area40530 Å2
ΔGint49 kcal/mol
Surface area45050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.288, 93.009, 98.914
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Xylose isomerase


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


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 298.5 K / Method: batch mode / pH: 7 / Details: Tris-HCl, ammonium sulfate, magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 126047 / % possible obs: 99 % / Redundancy: 12.7 % / CC1/2: 0.939 / CC star: 0.984 / Net I/σ(I): 15
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 1.76 / Num. unique obs: 6227 / CC1/2: 0.542 / CC star: 0.838 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IRK

6irk


Resolution: 1.5→49.46 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1658 1996 1.58 %
Rwork0.1487 123961 -
obs0.149 125957 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.47 Å2 / Biso mean: 15.0541 Å2 / Biso min: 1.22 Å2
Refinement stepCycle: final / Resolution: 1.5→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6082 0 230 634 6946
Biso mean--28.68 26.9 -
Num. residues----771
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.26441280.22388325845394
1.54-1.580.24481430.207287708913100
1.58-1.630.20251410.190188128953100
1.63-1.680.20521490.180887898938100
1.68-1.740.19741340.167488508984100
1.74-1.810.16231520.156188148966100
1.81-1.90.17151390.152988428981100
1.9-20.17741420.146588068948100
2-2.120.17651430.136288769019100
2.12-2.280.14981410.12888859026100
2.28-2.510.15361410.124689229063100
2.51-2.880.14581490.130889459094100
2.88-3.630.13371440.13590079151100
3.63-49.460.1591500.153593189468100

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