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- PDB-1clk: CRYSTAL STRUCTURE OF STREPTOMYCES DIASTATICUS NO.7 STRAIN M1033 X... -

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Basic information

Entry
Database: PDB / ID: 1clk
TitleCRYSTAL STRUCTURE OF STREPTOMYCES DIASTATICUS NO.7 STRAIN M1033 XYLOSE ISOMERASE AT 1.9 A RESOLUTION WITH PSEUDO-I222 SPACE GROUP
ComponentsXYLOSE ISOMERASE
KeywordsISOMERASE / XYLOSE ISOMERASE / GLUCOSE ISOMERASE / STREPTOMYCES / PSEUDO-I222
Function / homology
Function and homology information


xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion 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 diastaticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNiu, L. / Teng, M. / Zhu, X. / Gong, W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure of xylose isomerase from Streptomyces diastaticus no. 7 strain M1033 at 1.85 A resolution.
Authors: Zhu, X. / Teng, M. / Niu, L. / Xu, C. / Wang, Y.
#1: Journal: SCI.CHINA, SER.C: LIFE SCI. / Year: 1996
Title: Crystal Structure of Streptomyces diastaticus No.7 Strain M1033 Xylose Isomerase
Authors: Zhu, X. / Gong, W. / Niu, L. / Teng, M. / Xu, C. / Wu, C. / Cui, T. / Wang, Y. / Wang, C.
#2: Journal: Chin.Sci.Bull. / Year: 1991
Title: Growth of Single Crystals and Preliminary Analysis of Glucose Isomerase From Streptomyces M1033
Authors: Zhang, G.Y. / Niu, L.W. / Huang, W.Z. / Wang, C. / Liu, J. / Cui, Y. / Liu, X.A. / Wang, Y.Z. / Xu, X. / Liang, D.C.
History
DepositionApr 29, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_sheet / 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_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_ref_seq_dif.details / _struct_sheet.number_strands / _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)42,7933
Polymers42,7101
Non-polymers832
Water7,062392
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)171,17212
Polymers170,8394
Non-polymers3338
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area30240 Å2
ΔGint-194 kcal/mol
Surface area47680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)98.836, 93.927, 87.976
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 / D-GLUCOSE ISOMEARSE


Mass: 42709.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces diastaticus (bacteria) / Strain: STREPTOMYCES DIASTATICUS NO.7 STRAIN M1033 / References: UniProt: P50910, xylose isomerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Description: THE STRUCTURE HAS BEEN SOLVED IN PSEUDO-I222 SPACE GROUP. THE MOLECULE IS A TETRAMER CONTAINING ONE SUBUNITS IN THE ASYMMETRIC UNIT. TETRAMERS ARE POSITIONED ON THE 222 SYMMETRY SITE AT ...Description: THE STRUCTURE HAS BEEN SOLVED IN PSEUDO-I222 SPACE GROUP. THE MOLECULE IS A TETRAMER CONTAINING ONE SUBUNITS IN THE ASYMMETRIC UNIT. TETRAMERS ARE POSITIONED ON THE 222 SYMMETRY SITE AT THE ORIGIN OF THE CELL. THE STRUCTURE OF THE MONOMER IS AN EIGHT-FOLD ALPHA-BETA BARREL WITH AN EXTENDED C-TERMINAL LOOP WHICH FACILITATES AGGREGATION OF MONOMERS TO TETRAMERS.
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→5 Å / Num. obs: 25700 / % possible obs: 83.74 % / Redundancy: 2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.52
Reflection shellResolution: 1.9→1.98 Å / Mean I/σ(I) obs: 4.03 / % possible all: 75.56

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7XIA

7xia
PDB Unreleased entry


Resolution: 1.9→5 Å / Data cutoff low absF: 5 / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.186 --
obs-23381 76.2 %
Displacement parametersBiso mean: 19.95 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.9→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 2 392 3404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.251
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.2787 2582 -
obs--68 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO

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