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- PDB-2w90: Geobacillus stearothermophilus 6-phosphogluconate dehydrogenase w... -

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Basic information

Entry
Database: PDB / ID: 2w90
TitleGeobacillus stearothermophilus 6-phosphogluconate dehydrogenase with bound 6- phosphogluconate
Components6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
KeywordsOXIDOREDUCTASE / 6PDH / GEOBACILLUS / DEHYDROGENASE / PHSOPHOGLUCONATE
Function / homology
Function and homology information


6-Phosphogluconate Dehydrogenase, domain 3 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-PHOSPHOGLUCONIC ACID
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCameron, S. / Martini, V.P. / Iulek, J. / 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 16, 2012Group: Other
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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)105,1107
Polymers104,3972
Non-polymers7135
Water13,583754
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-100.2 kcal/mol
Surface area42850 Å2
MethodPQS
Unit cell
Length a, b, c (Å)66.950, 119.500, 142.240
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: 52198.641 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: phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Sugar ChemComp-6PG / 6-PHOSPHOGLUCONIC ACID


Type: D-saccharide / Mass: 276.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O10P
#3: 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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNOT IN UNIPROT, SEQUENCE OBTAINED BY BLAST WITH 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: 2.76 Å3/Da / Density % sol: 55.48 % / Description: NONE
Crystal growpH: 7.4 / Details: 0.2 M LISO4, 2.2 M (NH4)2SO4, 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: 2.2→50 Å / Num. obs: 57708 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.28 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.43
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 6.22 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.63 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZI0

2zi0


Resolution: 2.2→71.07 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.151 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2947 5.1 %RANDOM
Rwork0.171 ---
obs0.174 55339 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å20 Å2
2---2.8 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→71.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7344 0 43 754 8141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227907
X-RAY DIFFRACTIONr_bond_other_d0.0050.025439
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.97410772
X-RAY DIFFRACTIONr_angle_other_deg0.916313351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4351052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93724.348368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.318151429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4111549
X-RAY DIFFRACTIONr_chiral_restr0.0760.21187
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021595
X-RAY DIFFRACTIONr_nbd_refined0.2010.22045
X-RAY DIFFRACTIONr_nbd_other0.1850.25968
X-RAY DIFFRACTIONr_nbtor_refined0.1810.23868
X-RAY DIFFRACTIONr_nbtor_other0.0870.24183
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2648
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0280.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.250
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.91226426
X-RAY DIFFRACTIONr_mcbond_other0.17721989
X-RAY DIFFRACTIONr_mcangle_it1.16437809
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0434.53568
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.73362905
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: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 223 -
Rwork0.263 3954 -
obs--97.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.6237-0.24010.75364.1945-3.30678.8309-0.27180.13130.32360.4842-0.0229-0.4222-0.36140.57580.2946-0.1984-0.0025-0.0351-0.06760.0797-0.048439.7148-1.575131.5326
23.6367-1.4144-1.28960.99720.42880.6407-0.1017-0.0979-0.16370.0161-0.0538-0.1061-0.02280.34960.1555-0.1585-0.00050.0256-0.10160.0805-0.109625.05264.223.752
33.45191.16650.20524.5245-0.1972.68620.1927-0.8117-0.43451.5671-0.2769-0.49020.17470.53910.08410.41790.001-0.0830.08080.1012-0.20189.025410.601851.279
41.75260.148-0.42422.8633-0.29221.8074-0.0081-0.1665-0.1730.399-0.06190.0636-0.06270.11310.07-0.19710.0157-0.0082-0.23280.036-0.20126.080216.228634.598
51.4083-0.15420.18192.9998-0.72881.9054-0.02370.1278-0.2329-0.03160.00360.46620.06980.01390.0201-0.2634-0.0213-0.0016-0.2293-0.0207-0.1265-3.679616.893825.1733
64.9345-0.8146-0.37015.41250.24715.14660.18560.48810.0544-0.6399-0.12050.0597-0.2138-0.2828-0.065-0.08950.0463-0.0052-0.08040.0438-0.253515.877950.7906-1.2167
71.66540.3194-1.81013.7542-0.57314.16590.16180.04810.0517-0.1585-0.2529-0.4287-0.2110.41960.091-0.2668-0.0302-0.0137-0.10350.0172-0.169823.172246.297413.0982
82.18720.64230.00092.8069-0.05411.46490.10280.12370.10680.0174-0.04240.495-0.0909-0.05-0.0604-0.20920.01340.0084-0.24560.0112-0.1689-2.867234.087925.6724
91.40540.31420.21193.1885-0.71971.58010.1655-0.24720.1740.7262-0.09660.1672-0.28240.1869-0.069-0.0101-0.03440.0516-0.1727-0.0551-0.25313.84535.059339.045
108.7933-2.6706-3.53754.1511-5.090412.80150.3726-1.0889-0.59741.0902-0.559-1.80530.06471.00230.18640.3448-0.0885-0.47490.42590.09270.313723.656413.858353.0777
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 70
2X-RAY DIFFRACTION2A71 - 199
3X-RAY DIFFRACTION3A200 - 261
4X-RAY DIFFRACTION4A262 - 360
5X-RAY DIFFRACTION5A361 - 469
6X-RAY DIFFRACTION6B4 - 56
7X-RAY DIFFRACTION7B57 - 184
8X-RAY DIFFRACTION8B185 - 360
9X-RAY DIFFRACTION9B361 - 451
10X-RAY DIFFRACTION10B452 - 469

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