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- PDB-5lu7: Heptose isomerase GmhA mutant - D61A -

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Basic information

Entry
Database: PDB / ID: 5lu7
TitleHeptose isomerase GmhA mutant - D61A
ComponentsPhosphoheptose isomerase
KeywordsISOMERASE / Cooperativity / enzyme kinetics / hydrogen bonds / molecular modelling / quantum mechanics
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 / capsule polysaccharide biosynthetic process / carbohydrate derivative binding / zinc ion binding / cytoplasm
Similarity search - Function
Phosphoheptose isomerase / GmhA/DiaA / : / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-M7P / Phosphoheptose isomerase
Similarity search - Component
Biological speciesBurkholderia pseudomallei K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.92 Å
AuthorsVivoli, M. / Harmer, N.J. / Pang, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal Society2009/R2 United Kingdom
CitationJournal: Sci Rep / Year: 2017
Title: A half-site multimeric enzyme achieves its cooperativity without conformational changes.
Authors: Vivoli, M. / Pang, J. / Harmer, N.J.
History
DepositionSep 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoheptose isomerase
B: Phosphoheptose isomerase
C: Phosphoheptose isomerase
D: Phosphoheptose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,29217
Polymers83,1634
Non-polymers2,12913
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18100 Å2
ΔGint-211 kcal/mol
Surface area23740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.200, 83.680, 126.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Phosphoheptose isomerase / Heptose isomerase GmhA / Sedoheptulose 7-phosphate isomerase


Mass: 20790.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei K96243 (bacteria)
Gene: gmhA, BPSL2795 / Production host: Escherichia coli (E. coli)
References: UniProt: Q93UJ2, D-sedoheptulose-7-phosphate isomerase
#3: Sugar
ChemComp-M7P / 7-O-phosphono-D-glycero-alpha-D-manno-heptopyranose / D-GLYCERO-D-MANNOPYRANOSE-7-PHOSPHATE / 7-O-phosphono-D-glycero-alpha-D-manno-heptose / 7-O-phosphono-D-glycero-D-manno-heptose / 7-O-phosphono-D-glycero-manno-heptose


Type: D-saccharide, alpha linking / Mass: 290.162 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H15O10P

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Non-polymers , 4 types, 566 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 277 K / Method: batch mode
Details: untagged GmhA 10 mg per ml 0.1 M Na Acetate, pH 4.6, 8% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.92→50.33 Å / Num. obs: 59277 / % possible obs: 99.8 % / Redundancy: 5.5 % / Net I/σ(I): 17.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 1.92→37.542 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.62
RfactorNum. reflection% reflection
Rfree0.2148 2912 4.91 %
Rwork0.1703 --
obs0.1725 59262 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.92→37.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5708 0 123 557 6388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075929
X-RAY DIFFRACTIONf_angle_d1.0478010
X-RAY DIFFRACTIONf_dihedral_angle_d14.0772182
X-RAY DIFFRACTIONf_chiral_restr0.042942
X-RAY DIFFRACTIONf_plane_restr0.0061034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.95150.32351400.28782662X-RAY DIFFRACTION100
1.9515-1.98510.30181480.26312612X-RAY DIFFRACTION100
1.9851-2.02120.31931500.24842670X-RAY DIFFRACTION100
2.0212-2.06010.29831410.24582607X-RAY DIFFRACTION100
2.0601-2.10220.2854980.22822694X-RAY DIFFRACTION100
2.1022-2.14790.2971580.22662638X-RAY DIFFRACTION99
2.1479-2.19780.27651330.19832662X-RAY DIFFRACTION100
2.1978-2.25280.2621430.19372650X-RAY DIFFRACTION100
2.2528-2.31370.23231350.182650X-RAY DIFFRACTION100
2.3137-2.38180.23461260.18812675X-RAY DIFFRACTION100
2.3818-2.45860.25941560.17872668X-RAY DIFFRACTION100
2.4586-2.54650.23771440.17392652X-RAY DIFFRACTION100
2.5465-2.64840.20161230.16272684X-RAY DIFFRACTION100
2.6484-2.76890.21081320.16382681X-RAY DIFFRACTION100
2.7689-2.91480.24551410.17162720X-RAY DIFFRACTION100
2.9148-3.09740.2221330.16752675X-RAY DIFFRACTION100
3.0974-3.33640.22361350.16772703X-RAY DIFFRACTION100
3.3364-3.67190.2191390.15552701X-RAY DIFFRACTION100
3.6719-4.20260.15731490.13282732X-RAY DIFFRACTION100
4.2026-5.29250.14671380.12932753X-RAY DIFFRACTION100
5.2925-37.54880.16221500.15092861X-RAY DIFFRACTION99

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