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- PDB-4a8r: Protein crystallization and microgravity: glucose isomerase cryst... -

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Basic information

Entry
Database: PDB / ID: 4a8r
TitleProtein crystallization and microgravity: glucose isomerase crystals grown during the PCDF-PROTEIN mission
ComponentsXYLOSE ISOMERASE
KeywordsISOMERASE / MICROGRAVITY
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: 1.42 Å
AuthorsDecanniere, K. / Patino-Lopez, L.-D. / Sleutel, M. / Evrard, C. / Van De Weerdt, C. / Haumont, E. / Gavira, J.A. / Otalora, F. / Maes, D.
CitationJournal: To be Published
Title: Protein Crystallization and Microgravity: Glucose Isomerase Crystals Grown During the Pcdf-Protein Mission
Authors: Decanniere, K. / Patino-Lopez, L.-D. / Sleutel, M. / Evrard, C. / Van De Weerdt, C. / Haumont, E. / Gavira, J.A. / Otalora, F. / Maes, D.
History
DepositionNov 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)43,5855
Polymers43,2831
Non-polymers3024
Water8,233457
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)174,34120
Polymers173,1334
Non-polymers1,20816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation2_555-x,-y,z1
Buried area33680 Å2
ΔGint-226.4 kcal/mol
Surface area45750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.530, 98.220, 102.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein XYLOSE ISOMERASE / D-XYLOSE KETOL ISOMERASE


Mass: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) STREPTOMYCES RUBIGINOSUS (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOBALT (II) ION (CO): COBALT MOST LIKELY GIVEN THE ANOMALOUS SIGNAL AT TWO DIFFERENT WAVELENGTHS ...COBALT (II) ION (CO): COBALT MOST LIKELY GIVEN THE ANOMALOUS SIGNAL AT TWO DIFFERENT WAVELENGTHS GLYCEROL (GOL): TENTATIVE. SOME DENSITY IN THE ACTIVE SITE RUTHENIUM COMPOUND NOT OBSERVED IN ELECTRON DENSITY: BIS (2,2'-BIPYRIDINE)-4,4'-DICARBOXY-BIPYRIDINE-RUTHENIUM DI(N-SUCCINIMIDYL ESTER) BIS (HEXAFLUOROPHOSPHATE)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Description: STRUCTURE FACTOR FILE CONTAINS DATA TILL 0.897 ANGSTROM.
Crystal growpH: 7
Details: 28.7 MG/ML PROTEIN, 1.4 MG/ML PROTEIN COVALENTLY LABELED WITH A RUTHENIUM-CONTAINING LABEL, 0.9 M AMMONIUM SULPHATE, 100 MM HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.977
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 19, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.42→24.5 Å / Num. obs: 168537 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 42 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 52
Reflection shellResolution: 1.42→1.46 Å / Redundancy: 20 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 19 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GLK

2glk


Resolution: 1.42→70.77 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.021 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.12971 4334 5 %RANDOM
Rwork0.10291 ---
obs0.10426 82705 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.681 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.42→70.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 12 457 3485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.9614480
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4085436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9323.103174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.67315526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7151536
X-RAY DIFFRACTIONr_chiral_restr0.1390.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212649
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.4291.52009
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.24723226
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.36631272
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6174.51233
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.60733281
X-RAY DIFFRACTIONr_sphericity_free12.7113473
X-RAY DIFFRACTIONr_sphericity_bonded6.61733182
LS refinement shellResolution: 1.423→1.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.128 309 -
Rwork0.07 6054 -
obs--99.55 %

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