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- PDB-6nau: 1.55 Angstrom Resolution Crystal Structure of 6-phosphogluconolac... -

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Basic information

Entry
Database: PDB / ID: 6nau
Title1.55 Angstrom Resolution Crystal Structure of 6-phosphogluconolactonase from Klebsiella pneumoniae
Components6-phosphogluconolactonase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / 6-phosphogluconolactonase
Function / homology
Function and homology information


6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt, oxidative branch / glucose metabolic process / cytosol
Similarity search - Function
6-phosphogluconolactonase, YbhE-type / : / Lactonase, 7-bladed beta propeller / Lactonase, 7-bladed beta-propeller / Nitrous oxide reductase, N-terminal / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
6-phosphogluconolactonase / 6-phosphogluconolactonase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMinasov, G. / Shuvalova, L. / Pshenychnyi, S. / Dubrovska, I. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionDec 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-phosphogluconolactonase
B: 6-phosphogluconolactonase
C: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,76614
Polymers109,3883
Non-polymers1,37811
Water32,0491779
1
A: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0985
Polymers36,4631
Non-polymers6364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5694
Polymers36,4631
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0985
Polymers36,4631
Non-polymers6364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)184.745, 184.745, 48.761
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein 6-phosphogluconolactonase / 6-P-gluconolactonase


Mass: 36462.789 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: ybhE, pgl, NCTC9504_04578 / Plasmid: pMCSG53
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2X3FDC7, UniProt: A6T6J6*PLUS, 6-phosphogluconolactonase
#2: Chemical
ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1779 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 9.8 mg/ml, 0.01M Tris-HCl pH 8.3, Screen: PACT (F6), 0.2M Sodium formate, 0.1M Bis-Tris propane pH 6.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2018 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 138516 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.035 / Rrim(I) all: 0.106 / Rsym value: 0.1 / Χ2: 1.005 / Net I/σ(I): 20.5
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 6923 / CC1/2: 0.861 / Rpim(I) all: 0.258 / Rrim(I) all: 0.757 / Rsym value: 0.711 / Χ2: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QRJ

4qrj


Resolution: 1.55→29.33 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.283 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15552 6945 5 %RANDOM
Rwork0.12569 ---
obs0.12721 131376 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.521 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å20 Å2
2--0.07 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.55→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7698 0 83 1779 9560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0148538
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177407
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.66111739
X-RAY DIFFRACTIONr_angle_other_deg0.4491.64617454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51551116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.86923.045440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.217151308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1931546
X-RAY DIFFRACTIONr_chiral_restr0.070.21094
X-RAY DIFFRACTIONr_gen_planes_refined0.0420.0210041
X-RAY DIFFRACTIONr_gen_planes_other0.0390.021567
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.971.0164302
X-RAY DIFFRACTIONr_mcbond_other0.971.0164301
X-RAY DIFFRACTIONr_mcangle_it1.4261.5245472
X-RAY DIFFRACTIONr_mcangle_other1.4261.5245473
X-RAY DIFFRACTIONr_scbond_it2.1871.2664236
X-RAY DIFFRACTIONr_scbond_other2.1871.2664236
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3371.8066268
X-RAY DIFFRACTIONr_long_range_B_refined4.99814.799780
X-RAY DIFFRACTIONr_long_range_B_other4.51313.2739121
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 503 -
Rwork0.189 9664 -
obs--100 %

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