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- PDB-2w8z: Geobacillus stearothermophilus 6-phosphogluconate dehydrogenase w... -

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Basic information

Entry
Database: PDB / ID: 2w8z
TitleGeobacillus stearothermophilus 6-phosphogluconate dehydrogenase with bound 6- phosphogluconate
Components6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
KeywordsOXIDOREDUCTASE / 6PDH / PHSOPHOGLUCONATE / DEHYDROGENASE / GEOBACILLUS
Function / homology
Function and homology information


phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / D-gluconate metabolic process / phosphogluconate dehydrogenase (decarboxylating) activity / organic acid catabolic process / pentose-phosphate shunt / NADP binding
Similarity search - Function
6-Phosphogluconate Dehydrogenase, domain 3 / 6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase ...6-Phosphogluconate Dehydrogenase, domain 3 / 6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-PHOSPHOGLUCONIC ACID / 6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCameron, S. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Geobacillus Stearothermophilus 6-Phosphogluconate Dehydrogenase, Complexed with 6-Phosphogluconate.
Authors: Cameron, S. / Martini, V.P. / Iulek, J. / Hunter, W.N.
History
DepositionJan 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Derived calculations / Structure summary / Version format compliance
Revision 1.2Oct 16, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.3Dec 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
B: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1767
Polymers104,2832
Non-polymers8935
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12860 Å2
ΔGint-96.6 kcal/mol
Surface area41710 Å2
MethodPQS
Unit cell
Length a, b, c (Å)67.035, 119.965, 142.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING


Mass: 52141.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Description: ATCC/LGC-BIOCHEM / Plasmid: PET15B MODIFIED TO CONTAIN TEV CLEAVAGE SITE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS
References: UniProt: I3NI58*PLUS, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Sugar ChemComp-6PG / 6-PHOSPHOGLUCONIC ACID


Type: D-saccharide / Mass: 276.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O10P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNOT IN UNIPROT, SEQUENCE DERIVED BY BLAST AGAINST UNFINISHED GEOBACILLUS GENOME

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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: 2.8 Å3/Da / Density % sol: 55.5 % / Description: NONE
Crystal growpH: 7.4
Details: 0.2 M LITHIUM SULFATE, 2.2 M AMMONIUM SULFATE, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 17, 2007 / Details: TORODIAL FOCUSING MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→92.06 Å / Num. obs: 52157 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IYO

2iyo


Resolution: 2.3→71.43 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.813 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2618 5 %RANDOM
Rwork0.182 ---
obs0.185 49316 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.23 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å20 Å2
2---2.37 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.3→71.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7293 0 55 347 7695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227708
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.97310450
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04924.27356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96151368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1411548
X-RAY DIFFRACTIONr_chiral_restr0.1010.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025852
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.23786
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25247
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2493
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6171.54891
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06327602
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.55633208
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.434.52823
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 189 -
Rwork0.232 3578 -
obs--99.63 %

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