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- PDB-5by2: Sedoheptulose 7-phosphate isomerase from Colwellia psychrerythrae... -

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Basic information

Entry
Database: PDB / ID: 5by2
TitleSedoheptulose 7-phosphate isomerase from Colwellia psychrerythraea strain 34H
ComponentsPhosphoheptose isomeraseD-sedoheptulose 7-phosphate isomerase
KeywordsISOMERASE / CpsGmhA / Sedoheptulose 7-phosphate isomerase / Psychrophile / Colwellia psychrerythraea strain 34H
Function / homology
Function and homology information


D-sedoheptulose-7-phosphate isomerase / D-sedoheptulose 7-phosphate isomerase activity / D-glycero-D-manno-heptose 7-phosphate biosynthetic process / carbohydrate derivative binding / carbohydrate metabolic process / zinc ion binding / cytoplasm
Similarity search - Function
Phosphoheptose isomerase / GmhA/DiaA / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoheptose isomerase
Similarity search - Component
Biological speciesColwellia psychrerythraea 34H (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsLee, J.H. / Chang, J.H. / Do, H. / Yun, J.S.
CitationJournal: Mol.Cells / Year: 2015
Title: Crystal Structure and Comparative Sequence Analysis of GmhA from Colwellia psychrerythraea Strain 34H Provides Insight into Functional Similarity with DiaA
Authors: Do, H. / Yun, J.S. / Lee, C.W. / Choi, Y.J. / Kim, H.Y. / Kim, Y.J. / Park, H. / Chang, J.H. / Lee, J.H.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoheptose isomerase


Theoretical massNumber of molelcules
Total (without water)21,2221
Polymers21,2221
Non-polymers00
Water724
1
A: Phosphoheptose isomerase

A: Phosphoheptose isomerase

A: Phosphoheptose isomerase

A: Phosphoheptose isomerase


Theoretical massNumber of molelcules
Total (without water)84,8884
Polymers84,8884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area13940 Å2
ΔGint-74 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.310, 109.310, 44.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

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Components

#1: Protein Phosphoheptose isomerase / D-sedoheptulose 7-phosphate isomerase / Sedoheptulose 7-phosphate isomerase


Mass: 21221.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea 34H (bacteria)
Strain: 34H / Gene: gmhA, CPS_4434 / Production host: Escherichia coli (E. coli)
References: UniProt: Q47VU0, D-sedoheptulose-7-phosphate isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M Tris-HCl, 0.2 M magnesium chloride, 19%(v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97951 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.8→44.28 Å / Num. obs: 4651 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 11.8 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 13
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 7.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
Cootmodel building
RefinementResolution: 2.8→44.28 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 29.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2654 215 4.63 %RANDOM
Rwork0.2092 ---
obs0.2121 4643 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 0 0 4 1460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081476
X-RAY DIFFRACTIONf_angle_d1.0531999
X-RAY DIFFRACTIONf_dihedral_angle_d13.906540
X-RAY DIFFRACTIONf_chiral_restr0.05238
X-RAY DIFFRACTIONf_plane_restr0.005262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.52750.3269990.23112169X-RAY DIFFRACTION100
3.5275-44.28550.24371160.19982259X-RAY DIFFRACTION100

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