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- PDB-1oad: Glucose isomerase from Streptomyces rubiginosus in P21212 crystal form -

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Basic information

Entry
Database: PDB / ID: 1oad
TitleGlucose isomerase from Streptomyces rubiginosus in P21212 crystal form
ComponentsXYLOSE ISOMERASE
KeywordsISOMERASE / GLUCOSE ISOMERASE / XYLOSE ISOMERASE
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. / 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
: / 2-METHYLPENTANE-1,2,4-TRIOL / Xylose isomerase
Similarity search - Component
Biological speciesSTREPTOMYCES RUBIGINOSUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 Å
AuthorsRamagopal, U.A. / Dauter, M. / Dauter, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Sad Manganese in Two Crystal Forms of Glucose Isomerase
Authors: Ramagopal, U.A. / Dauter, M. / Dauter, Z.
History
DepositionJan 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
B: XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,47212
Polymers86,5692
Non-polymers90310
Water16,412911
1
A: XYLOSE ISOMERASE
B: XYLOSE ISOMERASE
hetero molecules

A: XYLOSE ISOMERASE
B: XYLOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,94424
Polymers173,1374
Non-polymers1,80720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.450, 129.590, 78.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.68035, -0.73289, 0.00093), (-0.73289, -0.68035, -0.001), (0.00137, -1)
Vector: 63.19709, 145.00256, 23.8181)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein XYLOSE ISOMERASE / GLUCOSE ISOMERASE


Mass: 43284.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) STREPTOMYCES RUBIGINOSUS (bacteria) / References: UniProt: P24300, xylose isomerase

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Non-polymers , 7 types, 921 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MQD / 2-METHYLPENTANE-1,2,4-TRIOL


Mass: 134.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 911 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL MET NOT VISIBLE, NEXT RESIDUE (ASN) WITHOUT SIDE

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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: 2.89 Å3/Da / Density % sol: 57 %
Crystal growpH: 7
Details: 17 MG/ML PROTEIN, 12 % MPD, 0.1 M MGCL2, 50 MM TRIS BUFFER PH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
135 mg/mlprotein1drop
220 mMTris1droppH7.0
325 %MPD1reservoir
40.2 M1reservoirMgCl2
50.1 MTris1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.54
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 20, 2002 / Details: FOCUSSING MIRROR
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→35 Å / Num. obs: 300270 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.6 / % possible all: 93.2
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 3.5 %
Reflection shell
*PLUS
% possible obs: 93.2 % / Rmerge(I) obs: 0.15

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Processing

Software
NameClassification
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
MLPHAREphasing
REFMACrefinement
RefinementMethod to determine structure: OTHER / Resolution: 1.5→20 Å / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.186 7880 5 %RANDOM
Rwork0.163 ---
obs0.163 157058 96.8 %-
Displacement parametersBiso mean: 17.2 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6079 0 54 911 7044
Refinement
*PLUS
Lowest resolution: 19.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.026
X-RAY DIFFRACTIONp_angle_d0.038
X-RAY DIFFRACTIONp_chiral_restr0.176
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.573 Å / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.254 / Num. reflection Rwork: 961 / Total num. of bins used: 20

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