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- PDB-1vp5: Crystal structure of 2,5-diketo-D-gluconic acid reductase (TM1009... -

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Basic information

Entry
Database: PDB / ID: 1vp5
TitleCrystal structure of 2,5-diketo-D-gluconic acid reductase (TM1009) from Thermotoga maritima at 2.40 A resolution
Components2,5-diketo-D-gluconic acid reductase
KeywordsOXIDOREDUCTASE / TM1009 / 2 / 5-diketo-d-gluconic acid reductase (ec 1.1.1.274) / structural genomics / Joint Center for Structural Genomics / JCSG / PSI / Protein Structure Initiative
Function / homology
Function and homology information


D-threo-aldose 1-dehydrogenase activity / aldose reductase (NADPH) activity / nucleotide binding / cytosol
Similarity search - Function
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Oxidoreductase, aldo/keto reductase family
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of 2,5-diketo-D-gluconic acid reductase (TM1009) from Thermotoga maritima at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 1.5May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,9874
Polymers69,5002
Non-polymers1,4872
Water4,197233
1
A: 2,5-diketo-D-gluconic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4932
Polymers34,7501
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2,5-diketo-D-gluconic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4932
Polymers34,7501
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.314, 94.314, 146.855
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 2 - 284 / Label seq-ID: 14 - 296

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

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Components

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


Mass: 34749.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1009 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0A2, 2,5-didehydrogluconate reductase (2-dehydro-D-gluconate-forming)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.73 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.6
Details: 5.0% Glycerol, 19.0% iso-Propanol, 19.0% PEG-4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.000034
DetectorType: ADSC / Detector: CCD / Date: Apr 3, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000034 Å / Relative weight: 1
ReflectionResolution: 2.4→24.93 Å / Num. obs: 28944 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 49.56 Å2 / Rsym value: 0.123 / Net I/σ(I): 15.6
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2124 / Rsym value: 0.83 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.2.0001refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: REFINEMENT STARTING MODEL

Resolution: 2.4→24.93 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.357 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20258 1471 5.1 %RANDOM
Rwork0.15113 ---
obs0.15363 27471 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.279 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.46 Å20 Å2
2--0.93 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.4→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4560 0 96 233 4889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224809
X-RAY DIFFRACTIONr_bond_other_d0.0020.024342
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.9636527
X-RAY DIFFRACTIONr_angle_other_deg0.94310079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9095567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99924.026231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73815835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9051533
X-RAY DIFFRACTIONr_chiral_restr0.0890.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025250
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02975
X-RAY DIFFRACTIONr_nbd_refined0.20.21010
X-RAY DIFFRACTIONr_nbd_other0.1920.24378
X-RAY DIFFRACTIONr_nbtor_other0.0890.22481
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.350.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.215
X-RAY DIFFRACTIONr_mcbond_it1.61632928
X-RAY DIFFRACTIONr_mcbond_other0.48631150
X-RAY DIFFRACTIONr_mcangle_it2.40654595
X-RAY DIFFRACTIONr_scbond_it4.76282179
X-RAY DIFFRACTIONr_scangle_it6.228111932
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4367 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal0.170.5
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 108 5.09 %
Rwork0.217 2014 -
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)
12.13770.2651-0.07652.32240.38432.1286-0.05270.2544-0.3859-0.1172-0.13120.04050.2423-0.22890.1839-0.1931-0.0120.0854-0.1508-0.0628-0.166662.560652.77620.8133
22.57540.2042-0.15391.90750.322.0959-0.0154-0.34360.19260.1768-0.18730.45270.1611-0.36710.2027-0.1699-0.0540.0222-0.0721-0.1212-0.131973.539525.0993-29.8503
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 28514 - 297
22BB2 - 28414 - 296

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