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- PDB-3cxr: Crystal structure of gluconate 5-dehydrogase from streptococcus s... -

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Basic information

Entry
Database: PDB / ID: 3cxr
TitleCrystal structure of gluconate 5-dehydrogase from streptococcus suis type 2
ComponentsDehydrogenase with different specificities
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)
Similarity search - Component
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPeng, H. / Gao, F. / Zhang, Q. / Liu, Y. / Gao, G.F.
CitationJournal: Protein Sci. / Year: 2009
Title: Structural insight into the catalytic mechanism of gluconate 5-dehydrogenase from Streptococcus suis: Crystal structures of the substrate-free and quaternary complex enzymes.
Authors: Zhang, Q. / Peng, H. / Gao, F. / Liu, Y. / Cheng, H. / Thompson, J. / Gao, G.F.
History
DepositionApr 25, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dehydrogenase with different specificities


Theoretical massNumber of molelcules
Total (without water)31,0561
Polymers31,0561
Non-polymers00
Water2,342130
1
A: Dehydrogenase with different specificities

A: Dehydrogenase with different specificities

A: Dehydrogenase with different specificities

A: Dehydrogenase with different specificities


Theoretical massNumber of molelcules
Total (without water)124,2264
Polymers124,2264
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area17390 Å2
ΔGint-127 kcal/mol
Surface area33600 Å2
MethodPISA
2
A: Dehydrogenase with different specificities

A: Dehydrogenase with different specificities


Theoretical massNumber of molelcules
Total (without water)62,1132
Polymers62,1132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3510 Å2
ΔGint-29 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.147, 75.378, 97.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Dehydrogenase with different specificities / Related to short-chain alcohol dehydrogenase


Mass: 31056.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: 05HAH33 / Gene: SSU05_1225, IdnO / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A4VVQ2, gluconate 5-dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.11 Å3/Da / Density % sol: 41.66 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→59.66 Å / Num. obs: 19757
Reflection shellResolution: 1.9→30.56 Å / Mean I/σ(I) obs: 4.2 / Num. unique all: 19757

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vl8

1vl8


Resolution: 2→30.56 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.905 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20772 888 5 %RANDOM
Rwork0.19111 ---
all0.21 ---
obs0.19193 16716 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2--0.33 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2→30.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 0 130 2068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221971
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9582667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5335258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82425.1979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23815328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.257157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021475
X-RAY DIFFRACTIONr_nbd_refined0.2130.2961
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21371
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.214
X-RAY DIFFRACTIONr_mcbond_it0.7241.51326
X-RAY DIFFRACTIONr_mcangle_it1.18222046
X-RAY DIFFRACTIONr_scbond_it2.0773738
X-RAY DIFFRACTIONr_scangle_it3.0264.5621
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 58 -
Rwork0.221 1193 -
obs--93.99 %

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