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- PDB-3awd: Crystal structure of gox2181 -

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Basic information

Entry
Database: PDB / ID: 3awd
TitleCrystal structure of gox2181
ComponentsPutative polyol dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
: / Putative polyol dehydrogenase
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAdam Yuan, Y. / Yuan, Z.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Biochemical and structural analysis of Gox2181, a new member of the SDR superfamily from Gluconobacter oxydans.
Authors: Liu, X. / Yuan, Z. / Adam Yuan, Y. / Lin, J. / Wei, D.
History
DepositionMar 18, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Putative polyol dehydrogenase
B: Putative polyol dehydrogenase
C: Putative polyol dehydrogenase
D: Putative polyol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7648
Polymers111,4914
Non-polymers2734
Water19,5281084
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14820 Å2
ΔGint-82 kcal/mol
Surface area33300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.273, 121.416, 136.546
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
Putative polyol dehydrogenase / gox2181


Mass: 27872.764 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Gene: GOX2181 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5FNX9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1084 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: PEG 8K MG, HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2010
RadiationMonochromator: 360 frames 1 degree oscillation / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.8→90.91 Å / Num. all: 92750 / Num. obs: 92746 / % possible obs: 99.64 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 24.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.03 / Num. unique all: 4828 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.875 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18448 4874 5 %RANDOM
Rwork0.15053 ---
all0.15224 92750 --
obs0.15224 92746 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.204 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2--1.35 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7704 0 4 1084 8792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227808
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.94310596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68151024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.55224.881336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26151316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8191552
X-RAY DIFFRACTIONr_chiral_restr0.0810.21244
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025860
X-RAY DIFFRACTIONr_nbd_refined0.1990.24140
X-RAY DIFFRACTIONr_nbtor_refined0.2980.25495
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2848
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.249
X-RAY DIFFRACTIONr_mcbond_it0.761.55251
X-RAY DIFFRACTIONr_mcangle_it1.128136
X-RAY DIFFRACTIONr_scbond_it2.04432937
X-RAY DIFFRACTIONr_scangle_it3.284.52460
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 350 -
Rwork0.204 6627 -
obs--97.48 %
Refinement TLS params.Method: refined / Origin x: 3.871 Å / Origin y: 50.734 Å / Origin z: 26.4957 Å
111213212223313233
T-0.1117 Å2-0.0162 Å20.0101 Å2--0.0987 Å2-0.0013 Å2---0.0971 Å2
L0.3513 °2-0.1228 °20.1588 °2-0.4033 °2-0.2352 °2--0.5157 °2
S-0.009 Å °0.0783 Å °-0.0427 Å °-0.002 Å °-0.055 Å °-0.0391 Å °0.0054 Å °0.0721 Å °0.064 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 257
2X-RAY DIFFRACTION1B1 - 257
3X-RAY DIFFRACTION1C1 - 257
4X-RAY DIFFRACTION1D1 - 257

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