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- PDB-3wbx: Crystal structure of Gox0644 at apoform -

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Basic information

Entry
Database: PDB / ID: 3wbx
TitleCrystal structure of Gox0644 at apoform
ComponentsPutative 2,5-diketo-D-gluconic acid reductase
KeywordsOXIDOREDUCTASE / Aldo-keto reductase (AKR) / reductase / NADPH
Function / homology
Function and homology information


2,5-didehydrogluconate reductase activity / small molecule metabolic process / organic substance metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / nucleotide binding
Similarity search - Function
Aldo-keto reductase family 5C2 / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 5C2 / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Putative 2,5-diketo-D-gluconic acid reductase
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYuan, Y.A. / Wang, C.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Gox0644 at apoform
Authors: Yuan, Y.A. / Wang, C.
History
DepositionMay 22, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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Assembly

Deposited unit
A: Putative 2,5-diketo-D-gluconic acid reductase
B: Putative 2,5-diketo-D-gluconic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4916
Polymers64,1072
Non-polymers3844
Water3,855214
1
A: Putative 2,5-diketo-D-gluconic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1492
Polymers32,0531
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative 2,5-diketo-D-gluconic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3414
Polymers32,0531
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.879, 75.780, 125.585
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 4 / Auth seq-ID: 9 - 279 / Label seq-ID: 12 - 282

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Putative 2,5-diketo-D-gluconic acid reductase


Mass: 32053.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Strain: 621H / Gene: GOX0644 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5FT75, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: PEG3350, LisSO4, Bis-tris, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 70 / Detector: CCD / Date: Jun 30, 2010
RadiationMonochromator: 360 degree collection, 1 degree oscillation / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 24390 / Num. obs: 24246 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.1 %
Reflection shellResolution: 2.3→2.38 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.843 / SU B: 18.582 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.931 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29997 1084 5.1 %RANDOM
Rwork0.22412 ---
all0.23 20430 --
obs0.22786 20012 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.598 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--1.06 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4366 0 20 214 4600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224480
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9576068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6655540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29523.929224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21915794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1581538
X-RAY DIFFRACTIONr_chiral_restr0.0830.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023422
X-RAY DIFFRACTIONr_nbd_refined0.1990.22092
X-RAY DIFFRACTIONr_nbtor_refined0.2960.22975
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.216
X-RAY DIFFRACTIONr_mcbond_it0.4621.52811
X-RAY DIFFRACTIONr_mcangle_it0.74324370
X-RAY DIFFRACTIONr_scbond_it1.1731930
X-RAY DIFFRACTIONr_scangle_it1.8294.51698
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2183 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.430.5
medium thermal0.462
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 79 -
Rwork0.247 1469 -
obs--98.72 %
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)
11.9682-0.0501-0.01861.06810.31411.4304-0.0675-0.1117-0.09980.10230.060.030.0665-0.06250.0074-0.1004-0.0188-0.0142-0.1154-0.0046-0.125412.1442.98628.8691
20.6704-0.06890.27082.2167-0.11092.10110.0582-0.01740.00930.0568-0.05180.15370.06950.0673-0.0064-0.09990.00920.0152-0.04870.0135-0.102217.03732.251340.3566
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 279
2X-RAY DIFFRACTION2B9 - 279

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