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- PDB-1qt1: CRYSTAL STRUCTURE OF XYLOSE ISOMERASE FROM STREPTOMYCES DIASTATIC... -

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Basic information

Entry
Database: PDB / ID: 1qt1
TitleCRYSTAL STRUCTURE OF XYLOSE ISOMERASE FROM STREPTOMYCES DIASTATICUS NO.7 M1033 AT 1.85 A RESOLUTION
ComponentsPROTEIN (XYLOSE ISOMERASE)
KeywordsISOMERASE / XYLOSE ISOMERASE / GLUCOSE ISOMERASE / STREPTOMYCES / TRUE SPACE GROUP
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: 1.85 Å
AuthorsNiu, L. / Teng, M. / Zhu, X.
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, Q. / Wu, C. / Cui, T. / Wang, Y.
#2: Journal: Chin.Sci.Bull. / Year: 1991
Title: Growth of Single Crystals and Preliminary Analysis of Glucose Isomerase from Streptomyces M1033
Authors: Zhang, G. / Niu, L. / Huang, W. / Wang, C. / Liu, X. / Wang, Y. / Xu, X. / Liang, D.
History
DepositionJun 29, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 29, 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 16, 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_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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 / _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: PROTEIN (XYLOSE ISOMERASE)
B: PROTEIN (XYLOSE ISOMERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6276
Polymers85,3912
Non-polymers2364
Water11,458636
1
A: PROTEIN (XYLOSE ISOMERASE)
B: PROTEIN (XYLOSE ISOMERASE)
hetero molecules

A: PROTEIN (XYLOSE ISOMERASE)
B: PROTEIN (XYLOSE ISOMERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,25412
Polymers170,7834
Non-polymers4718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area30440 Å2
ΔGint-215 kcal/mol
Surface area47300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)87.976, 98.836, 93.927
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: (0.999116, -0.042047, 0.000169), (-0.042047, -0.999116, -0.00025), (0.000179, 0.000243, -1)
Vector: -0.0046, 0.0114, 47.1745)
DetailsTHE MOLECULE IS A TETRAMER IN THE CRYSTAL CONTAINING TWO SUBUNITS IN THE ASYMMETRIC UNIT WHICH WERE REFINED INDEPENDENTLY. THE FIRST SUBUNIT IS NUMBERED FROM A 1 - A 387 AND THE SECOND SUBUNIT IS NUMBERED FROM B 501 - B 887. THE SUBUNITS ARE RELATED BY AN APPROXIMATE SYMMETRY. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B WHEN APPLIED TO CHAIN A.

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Components

#1: Protein PROTEIN (XYLOSE ISOMERASE) / D-XYLOSE KETOL ISOMERASE / D-GLUCOSE ISOMERASE


Mass: 42695.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces diastaticus (bacteria) / Strain: M1033 / References: UniProt: P50910, xylose isomerase
#2: Chemical
ChemComp-CO / COBALT (II) ION


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


Mass: 18.015 Da / Num. of mol.: 636 / 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: 48.53 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.02 MTris-HCl1drop
31.0 Mammonium sulfate1drop
40.01 M1dropMgCl2
50.001 M1dropCoCl2
60.02 MTris-HCl1reservoir
72.0 Mammonium sulfate1reservoir

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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: 1.85→5 Å / Num. obs: 55255 / % possible obs: 82.78 % / Redundancy: 4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.95
Reflection shellResolution: 1.85→1.93 Å / Mean I/σ(I) obs: 3.45 / % possible all: 72.83
Reflection shell
*PLUS
% possible obs: 72.8 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-GENdata reduction
X-GENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CLK

1clk


Resolution: 1.85→5 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.219 -10 %RANDOM
Rwork0.166 ---
obs0.166 52327 78.42 %-
Displacement parametersBiso mean: 12.54 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6018 0 4 636 6658
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.567
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
Refine LS restraints NCSNCS model details: RESTRAINS
LS refinement shellResolution: 1.85→1.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3327 -10 %
Rwork0.2638 5051 -
obs--68.6 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO OF X-PLOR3.1 / Topol file: TOPHCSDX.PRO OF X-PLOR3.1

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