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- PDB-4mh1: Crystal structure and functional studies of quinoprotein L-sorbos... -

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Basic information

Entry
Database: PDB / ID: 4mh1
TitleCrystal structure and functional studies of quinoprotein L-sorbose dehydrogenase from Ketogulonicigenium vulgare Y25
ComponentsSorbose dehydrogenase
KeywordsOXIDOREDUCTASE / 2-keto-L-gulonic acid / Ketogulonicigenium vulgare / L-sorbose dehydrogenase / Beta-Propeller / Hydrolase / Carbohydrate/Sugar Binding / periplasmic
Function / homology
Function and homology information


Quinoprotein alcohol dehydrogenase-like superfamily / Outer membrane protein assembly factor BamB / Pyrrolo-quinoline quinone repeat / 8 Propeller / Methanol Dehydrogenase; Chain A / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Mainly Beta
Similarity search - Domain/homology
PYRROLOQUINOLINE QUINONE / Sorbose dehydrogenase
Similarity search - Component
Biological speciesKetogulonicigenium vulgare (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHan, X. / Liu, X.
CitationJournal: Biotechnol.Lett. / Year: 2014
Title: Crystal structure of L-sorbose dehydrogenase, a pyrroloquinoline quinone-dependent enzyme with homodimeric assembly, from Ketogulonicigenium vulgare
Authors: Han, X. / Xiong, X. / Jiang, D. / Chen, S. / Huang, E. / Zhang, W. / Liu, X.
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorbose dehydrogenase
B: Sorbose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8974
Polymers122,5272
Non-polymers3702
Water00
1
A: Sorbose dehydrogenase
B: Sorbose dehydrogenase
hetero molecules

A: Sorbose dehydrogenase
B: Sorbose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,7948
Polymers245,0544
Non-polymers7414
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_554-y,-x,-z-11
Buried area9220 Å2
ΔGint-46 kcal/mol
Surface area63500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.530, 201.530, 201.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

#1: Protein Sorbose dehydrogenase / L-sorbose dehydrogenase


Mass: 61263.410 Da / Num. of mol.: 2 / Fragment: UNP residues 23-578 / Source method: isolated from a natural source / Source: (natural) Ketogulonicigenium vulgare (bacteria) / Strain: Y25 / References: UniProt: E3F069
#2: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6N2O8
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.7M ammonium sulfate, 5mM PQQ, 5mM CaCl2, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 22, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 37049 / % possible obs: 80 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 34.87 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.7-2.851100
2.85-3.21100
3.2-4.291100
4.29-7.321100
7.32-501100

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YiQ

1yiq


Resolution: 2.7→41.137 Å / FOM work R set: 0.8451 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 1991 5.14 %random
Rwork0.226 ---
obs0.2263 36754 99.48 %-
all-38745 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 9.07 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 141.59 Å2 / Biso mean: 38.69 Å2 / Biso min: 3.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7685 0 25 0 7710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097884
X-RAY DIFFRACTIONf_angle_d1.42110772
X-RAY DIFFRACTIONf_chiral_restr0.0931201
X-RAY DIFFRACTIONf_plane_restr0.0061424
X-RAY DIFFRACTIONf_dihedral_angle_d17.5722728
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7003-2.76780.28761390.302325722711100
2.7678-2.84260.29551400.296625812721100
2.8426-2.92630.27211400.277825972737100
2.9263-3.02070.28231400.259525722712100
3.0207-3.12860.25161410.250426022743100
3.1286-3.25380.26631400.225326012741100
3.2538-3.40180.25411410.238926042745100
3.4018-3.58110.23121430.226326222765100
3.5811-3.80530.29671360.27562500263695
3.8053-4.09890.19941390.21062568270798
4.0989-4.51090.16581430.16926532796100
4.5109-5.16260.16641460.167926752821100
5.1626-6.50020.24541470.228927202867100
6.5002-41.14190.21941560.209428873043100
Refinement TLS params.Method: refined / Origin x: 40.8943 Å / Origin y: -32.0454 Å / Origin z: -77.2712 Å
111213212223313233
T0.0288 Å2-0.0069 Å2-0.005 Å2-0.0517 Å20.0085 Å2--0.0158 Å2
L0.099 °20.0672 °20.1123 °2-0.2322 °20.0401 °2--0.2759 °2
S-0.0015 Å °0.0514 Å °0.0694 Å °-0.0084 Å °0.0156 Å °0.0152 Å °0.0029 Å °0.0847 Å °0.0339 Å °
Refinement TLS groupSelection details: ALL

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