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- PDB-5avn: The 1.03 angstrom structure (P212121) of glucose isomerase crysta... -

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Basic information

Entry
Database: PDB / ID: 5avn
TitleThe 1.03 angstrom structure (P212121) of glucose isomerase crystallized in high-strength agarose hydrogel
ComponentsXylose isomerase
KeywordsISOMERASE / Xylose isomerase / hydrogel
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
: / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsSugiyama, S. / Shimizu, N. / Maruyama, N. / Sazaki, G. / Adachi, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Matsumura, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS KAKENHI23860028 Japan
JSPS KAKENHI25650051 Japan
JSPS KAKENHI25286051 Japan
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Growth of protein crystals in hydrogels prevents osmotic shock
Authors: Sugiyama, S. / Maruyama, M. / Sazaki, G. / Hirose, M. / Adachi, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Matsumura, H.
History
DepositionJun 23, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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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)86,87810
Polymers86,3042
Non-polymers5748
Water19,0601058
1
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4395
Polymers43,1521
Non-polymers2874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4395
Polymers43,1521
Non-polymers2874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-108 kcal/mol
Surface area29310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.082, 98.285, 85.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-938-

HOH

31B-515-

HOH

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Components

#1: Protein Xylose isomerase / glucose isomerase


Mass: 43152.105 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1058 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5 / Details: 0.1 M Hepes-NaOH (pH 7.5), 1.75 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.03→50 Å / Num. obs: 386570 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.1
Reflection shellResolution: 1.03→1.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O1H

1o1h


Resolution: 1.03→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.743 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14969 16000 5 %RANDOM
Rwork0.12748 ---
obs0.1286 367026 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.697 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å2-0 Å2
2---0.29 Å2-0 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.03→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6092 0 24 1058 7174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0196721
X-RAY DIFFRACTIONr_bond_other_d0.0020.026191
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.9569160
X-RAY DIFFRACTIONr_angle_other_deg0.941314231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8075864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47822.923366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.579151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5521581
X-RAY DIFFRACTIONr_chiral_restr0.1290.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0218059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021690
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9070.8633330
X-RAY DIFFRACTIONr_mcbond_other1.6510.8593329
X-RAY DIFFRACTIONr_mcangle_it1.8621.2984236
X-RAY DIFFRACTIONr_mcangle_other1.8631.3014237
X-RAY DIFFRACTIONr_scbond_it2.1321.0363391
X-RAY DIFFRACTIONr_scbond_other2.0631.0343379
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7221.5064906
X-RAY DIFFRACTIONr_long_range_B_refined2.748.9189480
X-RAY DIFFRACTIONr_long_range_B_other2.4638.2858990
X-RAY DIFFRACTIONr_rigid_bond_restr8.439312912
X-RAY DIFFRACTIONr_sphericity_free19.8165227
X-RAY DIFFRACTIONr_sphericity_bonded6.062513775
LS refinement shellResolution: 1.03→1.057 Å
RfactorNum. reflection% reflection
Rfree0.242 1441 -
Rwork0.229 20000 -
obs--99.76 %

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