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- PDB-3u3h: X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed I... -

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Basic information

Entry
Database: PDB / ID: 3u3h
TitleX-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde
ComponentsXylose isomerase
KeywordsISOMERASE / Aldose-Ketose Isomerases / Glyceraldehyde / hydride shift / enzyme promiscuity
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
(2R)-propane-1,1,2,3-tetrol / FORMIC ACID / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsAllen, K.N. / Silvaggi, N.R. / Toteva, M.M. / Richard, J.P.
CitationJournal: Biochemistry / Year: 2011
Title: Binding Energy and Catalysis by d-Xylose Isomerase: Kinetic, Product, and X-ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde.
Authors: Toteva, M.M. / Silvaggi, N.R. / Allen, K.N. / Richard, J.P.
History
DepositionOct 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)43,6046
Polymers43,2831
Non-polymers3215
Water9,440524
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)174,41724
Polymers173,1334
Non-polymers1,28420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_576x,-y+2,-z+11
Buried area32890 Å2
ΔGint-147 kcal/mol
Surface area45160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.651, 98.148, 102.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Xylose 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

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Non-polymers , 5 types, 529 molecules

#2: Chemical ChemComp-03W / (2R)-propane-1,1,2,3-tetrol


Mass: 108.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O4
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 298 K / pH: 7
Details: 20mg/ml XI in water was mixed with an equal volume of well solution consisting of 0.2-0.3M Mg formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2005
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 0.97→19.972 Å / Num. obs: 272713 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 39.5
Reflection shellResolution: 1→1.04 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 6.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
EPMRphasing
PHENIX(phenix.refine: 1.7.2_858)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.97→19.97 Å / SU ML: 0.09 / σ(F): 1 / Phase error: 8.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.125 13001 4.96 %
Rwork0.116 --
obs0.116 262128 95.8 %
all-262140 -
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.5 Å2 / ksol: 0.45 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0497 Å20 Å20 Å2
2---0.1328 Å2-0 Å2
3---0.083 Å2
Refinement stepCycle: LAST / Resolution: 0.97→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 20 524 3585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083289
X-RAY DIFFRACTIONf_angle_d1.3434463
X-RAY DIFFRACTIONf_dihedral_angle_d13.3191235
X-RAY DIFFRACTIONf_chiral_restr0.075456
X-RAY DIFFRACTIONf_plane_restr0.009605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.9810.28043580.25927022X-RAY DIFFRACTION81
0.981-0.99250.26173870.23347526X-RAY DIFFRACTION88
0.9925-1.00460.22344130.20417830X-RAY DIFFRACTION91
1.0046-1.01730.19994100.18037908X-RAY DIFFRACTION92
1.0173-1.03070.18944290.15528012X-RAY DIFFRACTION93
1.0307-1.04480.14644140.13298062X-RAY DIFFRACTION94
1.0448-1.05980.13294070.11298156X-RAY DIFFRACTION94
1.0598-1.07560.11934360.09818167X-RAY DIFFRACTION95
1.0756-1.09240.0994170.08888276X-RAY DIFFRACTION96
1.0924-1.11030.09964130.08298259X-RAY DIFFRACTION96
1.1103-1.12940.09454490.07918362X-RAY DIFFRACTION96
1.1294-1.150.09374440.0758258X-RAY DIFFRACTION97
1.15-1.17210.08054640.0758357X-RAY DIFFRACTION97
1.1721-1.1960.09514500.07948343X-RAY DIFFRACTION97
1.196-1.2220.09194390.08218358X-RAY DIFFRACTION97
1.222-1.25040.09343930.08638478X-RAY DIFFRACTION97
1.2504-1.28170.10164220.098457X-RAY DIFFRACTION97
1.2817-1.31640.10584230.08938382X-RAY DIFFRACTION97
1.3164-1.35510.09734340.09148433X-RAY DIFFRACTION97
1.3551-1.39880.09594250.09488442X-RAY DIFFRACTION98
1.3988-1.44880.10174620.09648503X-RAY DIFFRACTION98
1.4488-1.50680.10094790.09638389X-RAY DIFFRACTION98
1.5068-1.57530.11114280.09748530X-RAY DIFFRACTION98
1.5753-1.65840.10634810.10068485X-RAY DIFFRACTION98
1.6584-1.76220.11444580.1058501X-RAY DIFFRACTION98
1.7622-1.89820.11834140.1148576X-RAY DIFFRACTION98
1.8982-2.0890.12264570.12068651X-RAY DIFFRACTION99
2.089-2.39080.11924630.11678653X-RAY DIFFRACTION99
2.3908-3.01060.14754620.13438765X-RAY DIFFRACTION99
3.0106-19.97660.1484700.14078986X-RAY DIFFRACTION99

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